chr6-32626411-A-T

Variant names:

• chr6-32626411-A-T
• rs9271768

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 0.273 in 150,958 control chromosomes in the GnomAD database, including 6,023 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 0.27 (6023 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.334 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: 0.273 AC: 41142 AN: 150842 Hom.: 6021 Cov.: 29

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.273 AC: 41171 AN: 150958 Hom.: 6023 Cov.: 29 AF XY: 0.270 AC XY: 19894 AN XY: 73712

African (AFR) AF: 0.201 AC: 8276 AN: 41172

American (AMR) AF: 0.323 AC: 4899 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1137 AN: 3452

East Asian (EAS) AF: 0.347 AC: 1764 AN: 5078

South Asian (SAS) AF: 0.252 AC: 1204 AN: 4770

European-Finnish (FIN) AF: 0.238 AC: 2477 AN: 10428

Middle Eastern (MID) AF: 0.228 AC: 66 AN: 290

European-Non Finnish (NFE) AF: 0.302 AC: 20415 AN: 67616

Other (OTH) AF: 0.268 AC: 560 AN: 2086

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	-0.90
CADD	Benign	6.2
DANN	Benign	0.32
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs9271768; hg19: chr6-32594188; COSMIC: COSV70073327;