rs7492028

chr13-96916842-C-Gchr13-96916842-C-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 0.261 in 152,072 control chromosomes in the GnomAD database, including 11,014 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 0.26 (11014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 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: 0.260 AC: 39536 AN: 151954 Hom.: 10981 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.261 AC: 39627 AN: 152072 Hom.: 11014 Cov.: 32 AF XY: 0.252 AC XY: 18743 AN XY: 74340

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.0269

Gnomad4 SAS AF: 0.0673

Gnomad4 FIN AF: 0.0433

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.224

Alfa AF: 0.0277 Hom.: 25

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.36
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7492028; hg19: chr13-97569096;