rs6545977

Positions:

• chr2-63074029-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.483

Alfa AF: 0.493 Hom.: 41287

Bravo AF: 0.487

Asia WGS AF: 0.292 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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