rs28772724

chr6-32541580-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.266

Alfa AF: 0.301 Hom.: 4785

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

Publications

LitVar

Other links and lift over

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