6-95769047-T-C

Position:

• chr6-95769047-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 0.915 in 152,282 control chromosomes in the GnomAD database, including 63,854 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 0.91 (63854 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 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: 0.915 AC: 139226 AN: 152164 Hom.: 63814 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.915 AC: 139323 AN: 152282 Hom.: 63854 Cov.: 33 AF XY: 0.913 AC XY: 67949 AN XY: 74450

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.922

Alfa AF: 0.932 Hom.: 3622

Bravo AF: 0.914

Asia WGS AF: 0.841 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1361900; hg19: chr6-96216923;