chr6-32543895-T-A

Variant names:

• chr6-32543895-T-A
• rs2157339

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 0.0623 in 145,388 control chromosomes in the GnomAD database, including 716 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 0.062 (716 hom., cov: 37)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0622 AC: 9040 AN: 145274 Hom.: 715 Cov.: 37

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0433

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.0268

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0673

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

GnomAD4 genome AF: 0.0623 AC: 9055 AN: 145388 Hom.: 716 Cov.: 37 AF XY: 0.0607 AC XY: 4299 AN XY: 70844

African (AFR) AF: 0.103 AC: 4097 AN: 39626

American (AMR) AF: 0.0535 AC: 757 AN: 14160

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 166 AN: 3366

East Asian (EAS) AF: 0.0341 AC: 164 AN: 4816

South Asian (SAS) AF: 0.0303 AC: 141 AN: 4646

European-Finnish (FIN) AF: 0.0417 AC: 408 AN: 9788

Middle Eastern (MID) AF: 0.0360 AC: 10 AN: 278

European-Non Finnish (NFE) AF: 0.0477 AC: 3141 AN: 65816

Other (OTH) AF: 0.0660 AC: 133 AN: 2014

Alfa AF: 0.0590 Hom.: 61

Asia WGS AF: 0.0420 AC: 146 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.38

Splicing

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

Other links and lift over

dbSNP: rs2157339; hg19: chr6-32511672;