6-37483920-G-T

Variant names:

• chr6-37483920-G-T
• rs904251
• NM_138493.3:c.191-631C>A

Variant summary

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

The NM_138493.3(CCDC167):​c.191-631C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 152,104 control chromosomes in the GnomAD database, including 23,205 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 0.52 (23205 hom., cov: 33)
• Consequence: CCDC167 NM_138493.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC167	NM_138493.3	c.191-631C>A		intron_variant	Intron 3 of 3	ENST00000373408.4	NP_612502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC167	ENST00000373408.4	c.191-631C>A		intron_variant	Intron 3 of 3	1	NM_138493.3	ENSP00000362507.3

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78799 AN: 151986 Hom.: 23203 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.554

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.518 AC: 78811 AN: 152104 Hom.: 23205 Cov.: 33 AF XY: 0.516 AC XY: 38349 AN XY: 74344

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.550

Alfa AF: 0.639 Hom.: 55546

Bravo AF: 0.507

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.021
DANN	Benign	0.49

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: rs904251; hg19: chr6-37451696;