rs2451563

Variant names:

• chr6-76404370-G-A
• rs2451563

Your query was ambiguous. Multiple possible variants found:

• chr6-76404370-G-A
• chr6-76404370-G-C

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 0.459 in 151,890 control chromosomes in the GnomAD database, including 19,786 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 0.46 (19786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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: 0.459 AC: 69672 AN: 151770 Hom.: 19778 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.459 AC: 69694 AN: 151890 Hom.: 19786 Cov.: 31 AF XY: 0.456 AC XY: 33869 AN XY: 74228

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.499

Alfa AF: 0.523 Hom.: 2847

Bravo AF: 0.446

Asia WGS AF: 0.429 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2451563; hg19: chr6-77114087; COSMIC: COSV69406001;