6-32698944-A-T

Variant names:

• chr6-32698944-A-T
• rs2856726

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 0.345 in 152,088 control chromosomes in the GnomAD database, including 9,492 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 0.35 (9492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52528 AN: 151970 Hom.: 9494 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.345 AC: 52540 AN: 152088 Hom.: 9492 Cov.: 32 AF XY: 0.340 AC XY: 25282 AN XY: 74370

African (AFR) AF: 0.334 AC: 13851 AN: 41476

American (AMR) AF: 0.331 AC: 5057 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2694 AN: 5168

South Asian (SAS) AF: 0.467 AC: 2246 AN: 4810

European-Finnish (FIN) AF: 0.189 AC: 2004 AN: 10600

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23851 AN: 67964

Other (OTH) AF: 0.392 AC: 828 AN: 2112

Alfa AF: 0.371 Hom.: 6011

Bravo AF: 0.355

Asia WGS AF: 0.488 AC: 1689 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2856726; hg19: chr6-32666721;