chr1-45500031-G-T

Variant names:

• chr1-45500031-G-T
• rs3748643
• ENST00000625766.2:n.-422C>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000625766.2(CCDC163):​n.-422C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 519,220 control chromosomes in the GnomAD database, including 135,946 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.74 (41787 hom., cov: 31)
  • Exomes 𝑓: 0.71 (94159 hom.)
• Consequence: CCDC163 ENST00000625766.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.682
• Publications: 20 publications found

Genes affected

CCDC163 (HGNC:27003): (CCDC163 homolog) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 1-45500031-G-T is Benign according to our data. Variant chr1-45500031-G-T is described in ClinVar as Benign. ClinVar VariationId is 684370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC163	NM_001102601.3	c.-422C>A		5_prime_UTR_variant	Exon 1 of 5	ENST00000629482.3	NP_001096071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC163	ENST00000629482.3	c.-422C>A		5_prime_UTR_variant	Exon 1 of 5	1	NM_001102601.3	ENSP00000486197.1

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112041 AN: 151912 Hom.: 41753 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.735

GnomAD4 exome AF: 0.711 AC: 260924 AN: 367190 Hom.: 94159 Cov.: 2 AF XY: 0.710 AC XY: 137491 AN XY: 193660

African (AFR) AF: 0.817 AC: 8828 AN: 10806

American (AMR) AF: 0.844 AC: 13692 AN: 16228

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 8296 AN: 11348

East Asian (EAS) AF: 0.950 AC: 22183 AN: 23342

South Asian (SAS) AF: 0.733 AC: 31623 AN: 43162

European-Finnish (FIN) AF: 0.675 AC: 14660 AN: 21720

Middle Eastern (MID) AF: 0.757 AC: 1222 AN: 1614

European-Non Finnish (NFE) AF: 0.667 AC: 145194 AN: 217706

Other (OTH) AF: 0.716 AC: 15226 AN: 21264

GnomAD4 genome AF: 0.738 AC: 112131 AN: 152030 Hom.: 41787 Cov.: 31 AF XY: 0.742 AC XY: 55143 AN XY: 74310

African (AFR) AF: 0.818 AC: 33937 AN: 41496

American (AMR) AF: 0.800 AC: 12224 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2545 AN: 3468

East Asian (EAS) AF: 0.942 AC: 4870 AN: 5170

South Asian (SAS) AF: 0.757 AC: 3647 AN: 4818

European-Finnish (FIN) AF: 0.678 AC: 7149 AN: 10544

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45289 AN: 67944

Other (OTH) AF: 0.737 AC: 1553 AN: 2108

Alfa AF: 0.590 Hom.: 1749

Bravo AF: 0.749

Asia WGS AF: 0.857 AC: 2979 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.72
PhyloP100		0.68
PromoterAI		-0.052	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3748643; hg19: chr1-45965703;