6-32137224-G-T

Variant names:

• chr6-32137224-G-T
• rs4713505

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 0.231 in 151,778 control chromosomes in the GnomAD database, including 5,240 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 0.23 (5240 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01
• Publications: 29 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 (AMR) allele frequency at 95% confidence interval = 0.293 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: 0.231 AC: 35103 AN: 151660 Hom.: 5240 Cov.: 30

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.231 AC: 35111 AN: 151778 Hom.: 5240 Cov.: 30 AF XY: 0.236 AC XY: 17482 AN XY: 74122

African (AFR) AF: 0.0550 AC: 2276 AN: 41410

American (AMR) AF: 0.301 AC: 4573 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3468

East Asian (EAS) AF: 0.163 AC: 840 AN: 5168

South Asian (SAS) AF: 0.190 AC: 912 AN: 4790

European-Finnish (FIN) AF: 0.385 AC: 4045 AN: 10500

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19826 AN: 67922

Other (OTH) AF: 0.253 AC: 531 AN: 2102

Alfa AF: 0.276 Hom.: 24653

Bravo AF: 0.220

Asia WGS AF: 0.201 AC: 700 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	0.19
DANN	Benign	0.38
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4713505; hg19: chr6-32105001;