6-32541580-G-T

Variant names:

• chr6-32541580-G-T
• rs28772724

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 0.272 in 147,338 control chromosomes in the GnomAD database, including 6,892 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 0.27 (6892 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 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: 0.272 AC: 40031 AN: 147228 Hom.: 6889 Cov.: 29

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.272 AC: 40055 AN: 147338 Hom.: 6892 Cov.: 29 AF XY: 0.270 AC XY: 19409 AN XY: 71848

African (AFR) AF: 0.179 AC: 7122 AN: 39820

American (AMR) AF: 0.337 AC: 4879 AN: 14466

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1138 AN: 3448

East Asian (EAS) AF: 0.360 AC: 1743 AN: 4848

South Asian (SAS) AF: 0.259 AC: 1233 AN: 4768

European-Finnish (FIN) AF: 0.252 AC: 2518 AN: 9978

Middle Eastern (MID) AF: 0.236 AC: 67 AN: 284

European-Non Finnish (NFE) AF: 0.306 AC: 20445 AN: 66804

Other (OTH) AF: 0.266 AC: 538 AN: 2026

Alfa AF: 0.296 Hom.: 6534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.50

Splicing

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

Other links and lift over

dbSNP: rs28772724; hg19: chr6-32509357; COSMIC: COSV69839743;