rs262467

Positions:

• chr6-120134624-T-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 0.421 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;