6-131462640-G-C

Variant names:

• chr6-131462640-G-C
• rs2608951

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 0.747 in 152,058 control chromosomes in the GnomAD database, including 43,846 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 0.75 (43846 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.885 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: 0.747 AC: 113474 AN: 151940 Hom.: 43834 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.747 AC: 113528 AN: 152058 Hom.: 43846 Cov.: 31 AF XY: 0.751 AC XY: 55824 AN XY: 74350

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.820

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.907

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.742

Alfa AF: 0.765 Hom.: 2609

Bravo AF: 0.731

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2608951; hg19: chr6-131783780;