6-32683763-C-T

Variant names:

• chr6-32683763-C-T
• rs17212223

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 0.194 in 152,102 control chromosomes in the GnomAD database, including 3,094 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 0.19 (3094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 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: 0.194 AC: 29549 AN: 151982 Hom.: 3094 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.194 AC: 29558 AN: 152102 Hom.: 3094 Cov.: 32 AF XY: 0.190 AC XY: 14092 AN XY: 74364

African (AFR) AF: 0.217 AC: 9006 AN: 41488

American (AMR) AF: 0.203 AC: 3108 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5166

South Asian (SAS) AF: 0.136 AC: 655 AN: 4824

European-Finnish (FIN) AF: 0.108 AC: 1144 AN: 10588

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13054 AN: 67964

Other (OTH) AF: 0.213 AC: 450 AN: 2114

Alfa AF: 0.178 Hom.: 4566

Bravo AF: 0.203

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.59
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17212223; hg19: chr6-32651540; COSMIC: COSV69193900;