rs201144856

Variant names:

• chr16-3031047-C-T
• rs201144856
• NM_001369667.1:c.386G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-3031047-C-T
• chr16-3031047-C-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001369667.1(BICDL2):​c.386G>A​(p.Arg129Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0034 in 1,540,310 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0023 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0035 (11 hom.)
• Consequence: BICDL2 NM_001369667.1 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.980
• Publications: 5 publications found

Genes affected

BICDL2 (HGNC:33584): (BICD family like cargo adaptor 2) Predicted to enable small GTPase binding activity. Predicted to be involved in Golgi to secretory granule transport and vesicle transport along microtubule. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.006970912).
• BP6: Variant 16-3031047-C-T is Benign according to our data. Variant chr16-3031047-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2646099.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 11 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001369667.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICDL2	NM_001369667.1	MANE Select	c.386G>A	p.Arg129Gln	missense	Exon 3 of 10	NP_001356596.1	A1A5D9-1
	BICDL2	NM_001103175.2		c.386G>A	p.Arg129Gln	missense	Exon 2 of 9	NP_001096645.1	A1A5D9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICDL2	ENST00000572449.6	TSL:5 MANE Select	c.386G>A	p.Arg129Gln	missense	Exon 3 of 10	ENSP00000459043.1	A1A5D9-1
	BICDL2	ENST00000389347.4	TSL:1	c.386G>A	p.Arg129Gln	missense	Exon 2 of 9	ENSP00000373998.4	A1A5D9-1
	BICDL2	ENST00000642419.1		c.485G>A	p.Arg162Gln	missense	Exon 4 of 11	ENSP00000493502.1	A0A2R8Y2X6

Frequencies

GnomAD3 genomes AF: 0.00231 AC: 351 AN: 152234 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000458

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00334

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00384

Gnomad OTH AF: 0.00430

GnomAD2 exomes AF: 0.00259 AC: 365 AN: 141182 AF XY: 0.00237

Gnomad AFR exome AF: 0.000809

Gnomad AMR exome AF: 0.00466

Gnomad ASJ exome AF: 0.000717

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000558

Gnomad NFE exome AF: 0.00387

Gnomad OTH exome AF: 0.00333

GnomAD4 exome AF: 0.00352 AC: 4887 AN: 1387958 Hom.: 11 Cov.: 32 AF XY: 0.00340 AC XY: 2331 AN XY: 685414

African (AFR) AF: 0.000600 AC: 19 AN: 31658

American (AMR) AF: 0.00484 AC: 174 AN: 35946

Ashkenazi Jewish (ASJ) AF: 0.000595 AC: 15 AN: 25216

East Asian (EAS) AF: 0.00 AC: 0 AN: 35812

South Asian (SAS) AF: 0.000239 AC: 19 AN: 79376

European-Finnish (FIN) AF: 0.000502 AC: 18 AN: 35878

Middle Eastern (MID) AF: 0.000176 AC: 1 AN: 5696

European-Non Finnish (NFE) AF: 0.00407 AC: 4401 AN: 1080358

Other (OTH) AF: 0.00414 AC: 240 AN: 58018

GnomAD4 genome AF: 0.00230 AC: 351 AN: 152352 Hom.: 1 Cov.: 33 AF XY: 0.00205 AC XY: 153 AN XY: 74494

African (AFR) AF: 0.000457 AC: 19 AN: 41580

American (AMR) AF: 0.00333 AC: 51 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4834

European-Finnish (FIN) AF: 0.000753 AC: 8 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00384 AC: 261 AN: 68028

Other (OTH) AF: 0.00425 AC: 9 AN: 2116

Alfa AF: 0.00253 Hom.: 2

Bravo AF: 0.00234

TwinsUK AF: 0.00270 AC: 10

ALSPAC AF: 0.00389 AC: 15

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.00211 AC: 17

ExAC AF: 0.000907 AC: 90

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.085
BayesDel_addAF	Benign	-0.59	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	21
DANN	Benign	0.76
DEOGEN2	Benign	0.0074	T
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.082
FATHMM_MKL	Benign	0.32	N
LIST_S2	Benign	0.78	T
MetaRNN	Benign	0.0070	T
MetaSVM	Benign	-0.89	T
PhyloP100		0.98
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-0.090	N
REVEL	Benign	0.051
Sift	Benign	0.85	T
Sift4G	Benign	0.38	T
Polyphen		0.41	B
Vest4		0.21
MVP		0.22
MPC		0.18
ClinPred		0.012	T
GERP RS		4.5
Varity_R		0.062
gMVP		0.65
Mutation Taster		=81/19	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs201144856; hg19: chr16-3081048; COSMIC: COSV54156470; COSMIC: COSV54156470;