Variant 6-37483138-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Variant links:

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]

CCDC167 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC167	NM_138493.3 linkuse as main transcript	c.*48A>G		3_prime_UTR_variant	4/4	ENST00000373408.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC167	ENST00000373408.4 linkuse as main transcript	c.*48A>G		3_prime_UTR_variant	4/4	1	NM_138493.3	P1

Frequencies

GnomAD3 genomes

AF:

0.723

AC:

109898

AN:

152018

Hom.:

40339

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.676

AC:

168989

AN:

249894

Hom.:

58053

AF XY:

0.672

AC XY:

90785

AN XY:

135042

show subpopulations

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 SAS exome

AF:

0.604

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.:

AF XY:

0.686

AC XY:

447317

AN XY:

652422

show subpopulations

Gnomad4 AFR exome

AF:

0.839

Gnomad4 AMR exome

AF:

0.708

Gnomad4 ASJ exome

AF:

0.793

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.605

Gnomad4 FIN exome

AF:

0.631

Gnomad4 NFE exome

AF:

0.698

Gnomad4 OTH exome

AF:

0.691

GnomAD4 genome

AF:

0.723

AC:

110010

AN:

152136

Hom.:

40394

Cov.:

AF XY:

0.716

AC XY:

53232

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.831

Gnomad4 AMR

AF:

0.730

Gnomad4 ASJ

AF:

0.784

Gnomad4 EAS

AF:

0.443

Gnomad4 SAS

AF:

0.582

Gnomad4 FIN

AF:

0.633

Gnomad4 NFE

AF:

0.697

Gnomad4 OTH

AF:

0.730

Alfa

AF:

0.714

Hom.:

50959

Bravo

AF:

0.737

Asia WGS

AF:

0.508

AC:

1765

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

Cadd

Benign

1.8

Dann

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over