6-95635211-T-G

Variant names:

• chr6-95635211-T-G
• rs4388292

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.798 in 152,018 control chromosomes in the GnomAD database, including 48,880 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 0.80 (48880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.849 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121233 AN: 151900 Hom.: 48857 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.798 AC: 121303 AN: 152018 Hom.: 48880 Cov.: 31 AF XY: 0.799 AC XY: 59319 AN XY: 74286

African (AFR) AF: 0.702 AC: 29067 AN: 41424

American (AMR) AF: 0.785 AC: 11995 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2995 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2954 AN: 5136

South Asian (SAS) AF: 0.815 AC: 3918 AN: 4810

European-Finnish (FIN) AF: 0.904 AC: 9575 AN: 10588

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58114 AN: 67998

Other (OTH) AF: 0.793 AC: 1677 AN: 2114

Alfa AF: 0.833 Hom.: 97235

Bravo AF: 0.782

Asia WGS AF: 0.732 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.1
DANN	Benign	0.71
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4388292; hg19: chr6-96083087;