2-63074029-G-A

Variant names:

• chr2-63074029-G-A
• rs6545977

Variant summary

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

The variant allele was found at a frequency of 0.496 in 151,638 control chromosomes in the GnomAD database, including 18,973 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 0.50 (18973 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75192 AN: 151522 Hom.: 18940 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.496 AC: 75275 AN: 151638 Hom.: 18973 Cov.: 31 AF XY: 0.497 AC XY: 36783 AN XY: 74050

African (AFR) AF: 0.512 AC: 21179 AN: 41358

American (AMR) AF: 0.476 AC: 7259 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2000 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1165 AN: 5054

South Asian (SAS) AF: 0.410 AC: 1964 AN: 4796

European-Finnish (FIN) AF: 0.588 AC: 6184 AN: 10514

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.499 AC: 33884 AN: 67902

Other (OTH) AF: 0.483 AC: 1019 AN: 2110

Alfa AF: 0.493 Hom.: 60354

Bravo AF: 0.487

Asia WGS AF: 0.292 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.37
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6545977; hg19: chr2-63301164; COSMIC: COSV50192764;