rs3828357

Positions:

• chr3-125929513-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024251.1(FAM86JP):​n.1530T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.358 in 1,596,110 control chromosomes in the GnomAD database, including 104,343 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.33 (8870 hom., cov: 32)
  • Exomes 𝑓: 0.36 (95473 hom.)
• Consequence: FAM86JP NR_024251.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.93

Genes affected

(HGNC:):

FAM86JP (HGNC:44097): (family with sequence similarity 86 member J, pseudogene)

ALG1L1P (HGNC:33721): (ALG1 like 1, pseudogene) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.013293445).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM86JP	NR_024251.1	n.1530T>C		non_coding_transcript_exon_variant	5/5
ALG1L1P	NR_171197.1	n.481A>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALG1L1P	ENST00000611639.4	n.652A>G		non_coding_transcript_exon_variant	7/7	3
	ENST00000692801.1	n.580A>G		non_coding_transcript_exon_variant	6/6
FAM86JP	ENST00000693415.1	n.1274T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50864 AN: 151892 Hom.: 8873 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.335

GnomAD3 exomes AF: 0.336 AC: 78478 AN: 233450 Hom.: 13891 AF XY: 0.341 AC XY: 43764 AN XY: 128302

Gnomad AFR exome AF: 0.262

Gnomad AMR exome AF: 0.234

Gnomad ASJ exome AF: 0.448

Gnomad EAS exome AF: 0.280

Gnomad SAS exome AF: 0.282

Gnomad FIN exome AF: 0.429

Gnomad NFE exome AF: 0.382

Gnomad OTH exome AF: 0.357

GnomAD4 exome AF: 0.360 AC: 520248 AN: 1444100 Hom.: 95473 Cov.: 73 AF XY: 0.360 AC XY: 258706 AN XY: 718794

Gnomad4 AFR exome AF: 0.258

Gnomad4 AMR exome AF: 0.243

Gnomad4 ASJ exome AF: 0.451

Gnomad4 EAS exome AF: 0.277

Gnomad4 SAS exome AF: 0.280

Gnomad4 FIN exome AF: 0.418

Gnomad4 NFE exome AF: 0.373

Gnomad4 OTH exome AF: 0.352

GnomAD4 genome AF: 0.335 AC: 50862 AN: 152010 Hom.: 8870 Cov.: 32 AF XY: 0.333 AC XY: 24723 AN XY: 74276

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.334

Alfa AF: 0.369 Hom.: 2102

Bravo AF: 0.321

TwinsUK AF: 0.385 AC: 1426

ALSPAC AF: 0.369 AC: 1421

ESP6500AA AF: 0.269 AC: 737

ESP6500EA AF: 0.361 AC: 1670

ExAC AF: 0.338 AC: 38777

Asia WGS AF: 0.263 AC: 915 AN: 3478

EpiCase AF: 0.379

EpiControl AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	14
DANN	Benign	0.96
Eigen	Benign	-0.38
Eigen_PC	Benign	-0.43
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.75	T;T
MetaRNN	Benign	0.013	T;T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	0.000048	P
PrimateAI	Uncertain	0.74	T
Sift4G	Uncertain	0.053	T;T
Polyphen		0.59	.;P
Vest4		0.14
MPC		0.0062
ClinPred		0.036	T
GERP RS		2.3
Varity_R		0.25
gMVP		0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs3828357; hg19: chr3-125648356; COSMIC: COSV61076292; COSMIC: COSV61076292;