6-92843819-G-T

Variant names:

• chr6-92843819-G-T
• rs6935730

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 0.556 in 152,040 control chromosomes in the GnomAD database, including 24,074 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 0.56 (24074 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84538 AN: 151926 Hom.: 24058 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.556 AC: 84590 AN: 152040 Hom.: 24074 Cov.: 33 AF XY: 0.556 AC XY: 41287 AN XY: 74294

African (AFR) AF: 0.530 AC: 21988 AN: 41458

American (AMR) AF: 0.651 AC: 9941 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2231 AN: 3472

East Asian (EAS) AF: 0.843 AC: 4347 AN: 5154

South Asian (SAS) AF: 0.613 AC: 2950 AN: 4812

European-Finnish (FIN) AF: 0.437 AC: 4618 AN: 10568

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36697 AN: 67984

Other (OTH) AF: 0.554 AC: 1170 AN: 2112

Alfa AF: 0.464 Hom.: 2168

Bravo AF: 0.573

Asia WGS AF: 0.704 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.49
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs6935730; hg19: chr6-93553537;