chr6-102231930-T-A

Variant names:

• chr6-102231930-T-A
• rs9498979

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00472 in 93,992 control chromosomes in the GnomAD database, including 2 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 0.0047 (2 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BS2: High Homozygotes in GnomAd4 at 2 gene

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: 0.00473 AC: 444 AN: 93894 Hom.: 2 Cov.: 26

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00205

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00125

Gnomad SAS AF: 0.00201

Gnomad FIN AF: 0.000394

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000898

Gnomad OTH AF: 0.00572

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

GnomAD4 genome AF: 0.00472 AC: 444 AN: 93992 Hom.: 2 Cov.: 26 AF XY: 0.00458 AC XY: 207 AN XY: 45172

African (AFR) AF: 0.0106 AC: 378 AN: 35784

American (AMR) AF: 0.00205 AC: 17 AN: 8280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1500

East Asian (EAS) AF: 0.00125 AC: 2 AN: 1600

South Asian (SAS) AF: 0.00201 AC: 4 AN: 1994

European-Finnish (FIN) AF: 0.000394 AC: 2 AN: 5076

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 144

European-Non Finnish (NFE) AF: 0.000898 AC: 34 AN: 37856

Other (OTH) AF: 0.00568 AC: 7 AN: 1232

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.17
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9498979; hg19: chr6-102679805;