rs2451563

chr6-76404370-G-Achr6-76404370-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;