6-32888705-T-C

Variant names:

• chr6-32888705-T-C
• rs1029295

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 0.139 in 152,254 control chromosomes in the GnomAD database, including 1,753 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 0.14 (1753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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: 0.139 AC: 21122 AN: 152136 Hom.: 1748 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.139 AC: 21164 AN: 152254 Hom.: 1753 Cov.: 32 AF XY: 0.140 AC XY: 10393 AN XY: 74448

African (AFR) AF: 0.222 AC: 9229 AN: 41518

American (AMR) AF: 0.100 AC: 1533 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.0882 AC: 458 AN: 5190

South Asian (SAS) AF: 0.154 AC: 745 AN: 4830

European-Finnish (FIN) AF: 0.113 AC: 1204 AN: 10612

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.103 AC: 6975 AN: 68024

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.113 Hom.: 3400

Bravo AF: 0.138

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1029295; hg19: chr6-32856482;