NM_138493.3:c.191-631C>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 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 (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC167	NM_138493.3	MANE Select	c.191-631C>A		intron	N/A	NP_612502.1	Q9P0B6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC167	ENST00000373408.4	TSL:1 MANE Select	c.191-631C>A		intron	N/A	ENSP00000362507.3	Q9P0B6
	CCDC167	ENST00000916247.1		c.188-631C>A		intron	N/A	ENSP00000586306.1

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

African (AFR) AF: 0.223 AC: 9240 AN: 41496

American (AMR) AF: 0.611 AC: 9340 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2420 AN: 3472

East Asian (EAS) AF: 0.441 AC: 2276 AN: 5164

South Asian (SAS) AF: 0.525 AC: 2531 AN: 4824

European-Finnish (FIN) AF: 0.607 AC: 6427 AN: 10584

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44527 AN: 67960

Other (OTH) AF: 0.550 AC: 1163 AN: 2116

Alfa AF: 0.607 Hom.: 88550

Bravo AF: 0.507

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.021
DANN	Benign	0.49
PhyloP100		-3.5
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: rs904251; hg19: chr6-37451696;