6-32792668-G-T

Variant names:

• chr6-32792668-G-T
• rs2621382

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 0.615 in 151,968 control chromosomes in the GnomAD database, including 28,911 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 0.61 (28911 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.693 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: 0.615 AC: 93345 AN: 151850 Hom.: 28896 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.615 AC: 93399 AN: 151968 Hom.: 28911 Cov.: 32 AF XY: 0.620 AC XY: 46054 AN XY: 74282

African (AFR) AF: 0.639 AC: 26464 AN: 41426

American (AMR) AF: 0.577 AC: 8822 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3591 AN: 5170

South Asian (SAS) AF: 0.713 AC: 3435 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7163 AN: 10536

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39666 AN: 67954

Other (OTH) AF: 0.613 AC: 1294 AN: 2112

Alfa AF: 0.589 Hom.: 7190

Bravo AF: 0.606

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.023
DANN	Benign	0.45
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2621382; hg19: chr6-32760445;