9-15578865-G-A

Variant names:

• chr9-15578865-G-A
• rs79217038
• NM_173550.4:c.194G>A

Variant summary

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

The NM_173550.4(CCDC171):​c.194G>A​(p.Ser65Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00817 in 1,613,186 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0054 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0085 (79 hom.)
• Consequence: CCDC171 NM_173550.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.76
• Publications: 6 publications found

Genes affected

CCDC171 (HGNC:29828): (coiled-coil domain containing 171)

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=0.0063900054).
• BP6: Variant 9-15578865-G-A is Benign according to our data. Variant chr9-15578865-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2659091.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173550.4. 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
	CCDC171	NM_173550.4	MANE Select	c.194G>A	p.Ser65Asn	missense	Exon 4 of 26	NP_775821.2
	CCDC171	NM_001355547.1		c.194G>A	p.Ser65Asn	missense	Exon 3 of 25	NP_001342476.1	Q6TFL3-4
	CCDC171	NM_001348002.2		c.-248G>A		5_prime_UTR	Exon 4 of 27	NP_001334931.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC171	ENST00000380701.8	TSL:1 MANE Select	c.194G>A	p.Ser65Asn	missense	Exon 4 of 26	ENSP00000370077.3	Q6TFL3-1
	CCDC171	ENST00000905141.1		c.194G>A	p.Ser65Asn	missense	Exon 4 of 26	ENSP00000575200.1
	CCDC171	ENST00000971281.1		c.194G>A	p.Ser65Asn	missense	Exon 4 of 26	ENSP00000641340.1

Frequencies

GnomAD3 genomes AF: 0.00543 AC: 826 AN: 152180 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00135

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00413

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00928

Gnomad OTH AF: 0.00526

GnomAD2 exomes AF: 0.00557 AC: 1393 AN: 250236 AF XY: 0.00557

Gnomad AFR exome AF: 0.00228

Gnomad AMR exome AF: 0.00289

Gnomad ASJ exome AF: 0.0000996

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00917

Gnomad NFE exome AF: 0.00899

Gnomad OTH exome AF: 0.00625

GnomAD4 exome AF: 0.00845 AC: 12349 AN: 1460888 Hom.: 79 Cov.: 30 AF XY: 0.00824 AC XY: 5989 AN XY: 726792

African (AFR) AF: 0.00132 AC: 44 AN: 33424

American (AMR) AF: 0.00294 AC: 131 AN: 44590

Ashkenazi Jewish (ASJ) AF: 0.000230 AC: 6 AN: 26100

East Asian (EAS) AF: 0.00 AC: 0 AN: 39616

South Asian (SAS) AF: 0.000139 AC: 12 AN: 86146

European-Finnish (FIN) AF: 0.00826 AC: 441 AN: 53382

Middle Eastern (MID) AF: 0.00104 AC: 6 AN: 5760

European-Non Finnish (NFE) AF: 0.0101 AC: 11269 AN: 1111518

Other (OTH) AF: 0.00729 AC: 440 AN: 60352

GnomAD4 genome AF: 0.00542 AC: 826 AN: 152298 Hom.: 4 Cov.: 32 AF XY: 0.00522 AC XY: 389 AN XY: 74472

African (AFR) AF: 0.00135 AC: 56 AN: 41582

American (AMR) AF: 0.00412 AC: 63 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4820

European-Finnish (FIN) AF: 0.00603 AC: 64 AN: 10608

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

European-Non Finnish (NFE) AF: 0.00928 AC: 631 AN: 68022

Other (OTH) AF: 0.00521 AC: 11 AN: 2112

Alfa AF: 0.00774 Hom.: 10

Bravo AF: 0.00543

TwinsUK AF: 0.00863 AC: 32

ALSPAC AF: 0.00934 AC: 36

ESP6500AA AF: 0.00318 AC: 14

ESP6500EA AF: 0.00756 AC: 65

ExAC AF: 0.00570 AC: 692

Asia WGS AF: 0.000289 AC: 2 AN: 3478

EpiCase AF: 0.00727

EpiControl AF: 0.00701

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	0.15
BayesDel_addAF	Benign	-0.56	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	21
DANN	Benign	0.96
DEOGEN2	Benign	0.027	T
Eigen	Benign	-0.31
Eigen_PC	Benign	-0.12
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.75	T
M_CAP	Benign	0.0068	T
MetaRNN	Benign	0.0064	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.5	L
PhyloP100		2.8
PrimateAI	Uncertain	0.48	T
PROVEAN	Benign	-0.39	N
REVEL	Benign	0.031
Sift	Benign	0.41	T
Sift4G	Benign	0.66	T
Polyphen		0.0060	B
Vest4		0.49
MVP		0.061
ClinPred		0.0088	T
GERP RS		4.3
Varity_R		0.081
gMVP		0.068
Mutation Taster		=98/2	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: rs79217038; hg19: chr9-15578863;