rs6545977

Variant names:

• chr2-63074029-G-A
• rs6545977

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;