6-95817279-A-T

Variant names:

• chr6-95817279-A-T
• rs4840081

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 0.925 in 152,224 control chromosomes in the GnomAD database, including 65,415 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 0.92 (65415 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 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: 0.925 AC: 140702 AN: 152106 Hom.: 65389 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.925 AC: 140776 AN: 152224 Hom.: 65415 Cov.: 32 AF XY: 0.924 AC XY: 68800 AN XY: 74438

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.990

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.935

Alfa AF: 0.947 Hom.: 8502

Bravo AF: 0.918

Asia WGS AF: 0.898 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.070
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4840081; hg19: chr6-96265155;