rs262467

Variant names:

• chr6-120134624-T-C
• rs262467

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 0.421 in 151,930 control chromosomes in the GnomAD database, including 14,899 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 0.42 (14899 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

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 (EAS) allele frequency at 95% confidence interval = 0.572 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: 0.421 AC: 63916 AN: 151810 Hom.: 14900 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.421 AC: 63940 AN: 151930 Hom.: 14899 Cov.: 31 AF XY: 0.428 AC XY: 31816 AN XY: 74262

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.434

Alfa AF: 0.435 Hom.: 1831

Bravo AF: 0.405

Asia WGS AF: 0.564 AC: 1958 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs262467; hg19: chr6-120455770;