chr6-37483138-T-C

Variant names:

• chr6-37483138-T-C
• rs10692
• NM_138493.3:c.*48A>G

Variant summary

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

The NM_138493.3(CCDC167):​c.*48A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 1,445,532 control chromosomes in the GnomAD database, including 349,602 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 0.72 (40394 hom., cov: 33)
  • Exomes 𝑓: 0.69 (309208 hom.)
• Consequence: CCDC167 NM_138493.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 19 publications found

Genes affected

CCDC167 (HGNC:21239): (coiled-coil domain containing 167) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (REVEL=0.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138493.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC167	NM_138493.3	MANE Select	c.*48A>G		3_prime_UTR	Exon 4 of 4	NP_612502.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC167	ENST00000373408.4	TSL:1 MANE Select	c.*48A>G		3_prime_UTR	Exon 4 of 4	ENSP00000362507.3

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109898 AN: 152018 Hom.: 40339 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.736

GnomAD2 exomes AF: 0.676 AC: 168989 AN: 249894 AF XY: 0.672

Gnomad AFR exome AF: 0.838

Gnomad AMR exome AF: 0.703

Gnomad ASJ exome AF: 0.788

Gnomad EAS exome AF: 0.445

Gnomad FIN exome AF: 0.634

Gnomad NFE exome AF: 0.700

Gnomad OTH exome AF: 0.684

GnomAD4 exome AF: 0.688 AC: 890214 AN: 1293396 Hom.: 309208 Cov.: 18 AF XY: 0.686 AC XY: 447317 AN XY: 652422

African (AFR) AF: 0.839 AC: 25271 AN: 30126

American (AMR) AF: 0.708 AC: 31374 AN: 44296

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 19838 AN: 25018

East Asian (EAS) AF: 0.490 AC: 18991 AN: 38782

South Asian (SAS) AF: 0.605 AC: 50065 AN: 82798

European-Finnish (FIN) AF: 0.631 AC: 33564 AN: 53180

Middle Eastern (MID) AF: 0.792 AC: 4352 AN: 5494

European-Non Finnish (NFE) AF: 0.698 AC: 668862 AN: 958890

Other (OTH) AF: 0.691 AC: 37897 AN: 54812

GnomAD4 genome AF: 0.723 AC: 110010 AN: 152136 Hom.: 40394 Cov.: 33 AF XY: 0.716 AC XY: 53232 AN XY: 74374

African (AFR) AF: 0.831 AC: 34522 AN: 41528

American (AMR) AF: 0.730 AC: 11165 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2282 AN: 5152

South Asian (SAS) AF: 0.582 AC: 2797 AN: 4806

European-Finnish (FIN) AF: 0.633 AC: 6702 AN: 10596

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47351 AN: 67974

Other (OTH) AF: 0.730 AC: 1537 AN: 2106

Alfa AF: 0.714 Hom.: 69320

Bravo AF: 0.737

Asia WGS AF: 0.508 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-1.4
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: rs10692; hg19: chr6-37450914; COSMIC: COSV64982259; COSMIC: COSV64982259;