chr6-32715138-T-G

Variant names:

• chr6-32715138-T-G
• rs3997854

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 0.164 in 152,076 control chromosomes in the GnomAD database, including 2,417 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 0.16 (2417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 21 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 (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.164 AC: 24938 AN: 151958 Hom.: 2415 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.164 AC: 24973 AN: 152076 Hom.: 2417 Cov.: 32 AF XY: 0.163 AC XY: 12143 AN XY: 74350

African (AFR) AF: 0.276 AC: 11449 AN: 41470

American (AMR) AF: 0.142 AC: 2171 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3472

East Asian (EAS) AF: 0.0822 AC: 426 AN: 5180

South Asian (SAS) AF: 0.0664 AC: 320 AN: 4818

European-Finnish (FIN) AF: 0.155 AC: 1640 AN: 10566

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7840 AN: 67962

Other (OTH) AF: 0.146 AC: 309 AN: 2114

Alfa AF: 0.127 Hom.: 1299

Bravo AF: 0.178

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.33
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs3997854; hg19: chr6-32682915;