rs1539172

Variant names:

• chr9-15784633-A-G
• rs1539172
• NM_173550.4:c.3206A>G

Your query was ambiguous. Multiple possible variants found:

• chr9-15784633-A-G
• chr9-15784633-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173550.4(CCDC171):​c.3206A>G​(p.Lys1069Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 1,610,944 control chromosomes in the GnomAD database, including 197,617 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.50 (18871 hom., cov: 32)
  • Exomes 𝑓: 0.49 (178746 hom.)
• Consequence: CCDC171 NM_173550.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44
• Publications: 41 publications found

Genes affected

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

LOC107987049 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=5.2969528E-5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC171	NM_173550.4	c.3206A>G	p.Lys1069Arg	missense_variant	Exon 21 of 26	ENST00000380701.8	NP_775821.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC171	ENST00000380701.8	c.3206A>G	p.Lys1069Arg	missense_variant	Exon 21 of 26	1	NM_173550.4	ENSP00000370077.3
CCDC171	ENST00000449575.6	c.923A>G	p.Lys308Arg	missense_variant	Exon 5 of 11	2		ENSP00000409055.2
CCDC171	ENST00000432954.1	c.365A>G	p.Lys122Arg	missense_variant	Exon 3 of 6	2		ENSP00000399526.1

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75194 AN: 151766 Hom.: 18837 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.469

GnomAD2 exomes AF: 0.465 AC: 116653 AN: 250714 AF XY: 0.474

Gnomad AFR exome AF: 0.555

Gnomad AMR exome AF: 0.304

Gnomad ASJ exome AF: 0.463

Gnomad EAS exome AF: 0.350

Gnomad FIN exome AF: 0.450

Gnomad NFE exome AF: 0.496

Gnomad OTH exome AF: 0.471

GnomAD4 exome AF: 0.492 AC: 717812 AN: 1459060 Hom.: 178746 Cov.: 36 AF XY: 0.494 AC XY: 358611 AN XY: 725966

African (AFR) AF: 0.561 AC: 18744 AN: 33414

American (AMR) AF: 0.318 AC: 14181 AN: 44652

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 12113 AN: 26092

East Asian (EAS) AF: 0.344 AC: 13650 AN: 39648

South Asian (SAS) AF: 0.560 AC: 48266 AN: 86126

European-Finnish (FIN) AF: 0.458 AC: 24438 AN: 53320

Middle Eastern (MID) AF: 0.521 AC: 3003 AN: 5762

European-Non Finnish (NFE) AF: 0.499 AC: 553732 AN: 1109744

Other (OTH) AF: 0.492 AC: 29685 AN: 60302

GnomAD4 genome AF: 0.496 AC: 75280 AN: 151884 Hom.: 18871 Cov.: 32 AF XY: 0.489 AC XY: 36308 AN XY: 74248

African (AFR) AF: 0.552 AC: 22850 AN: 41428

American (AMR) AF: 0.406 AC: 6195 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3468

East Asian (EAS) AF: 0.345 AC: 1782 AN: 5158

South Asian (SAS) AF: 0.540 AC: 2603 AN: 4816

European-Finnish (FIN) AF: 0.431 AC: 4550 AN: 10556

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33908 AN: 67892

Other (OTH) AF: 0.471 AC: 991 AN: 2106

Alfa AF: 0.490 Hom.: 90755

Bravo AF: 0.491

TwinsUK AF: 0.488 AC: 1809

ALSPAC AF: 0.514 AC: 1982

ESP6500AA AF: 0.558 AC: 2459

ESP6500EA AF: 0.500 AC: 4297

ExAC AF: 0.478 AC: 57985

Asia WGS AF: 0.494 AC: 1713 AN: 3478

EpiCase AF: 0.501

EpiControl AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.058
BayesDel_addAF	Benign	-0.56	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Benign	0.10
DEOGEN2	Benign	0.016	T
Eigen	Benign	-0.14
Eigen_PC	Benign	-0.023
FATHMM_MKL	Benign	0.18	N
LIST_S2	Benign	0.11	T
MetaRNN	Benign	0.000053	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	0.26	N
PhyloP100		3.4
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	0.010	N
REVEL	Benign	0.096
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.032
ClinPred		0.0039	T
GERP RS		4.1
Varity_R		0.057
gMVP		0.089
Mutation Taster		=100/0	polymorphism (auto)

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: rs1539172; hg19: chr9-15784631; COSMIC: COSV52634248;