rs4772972

Variant names:

• chr13-108458066-C-T
• rs4772972

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 0.175 in 152,058 control chromosomes in the GnomAD database, including 3,067 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 0.18 (3067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 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: 0.175 AC: 26627 AN: 151940 Hom.: 3069 Cov.: 31

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.175 AC: 26619 AN: 152058 Hom.: 3067 Cov.: 31 AF XY: 0.172 AC XY: 12801 AN XY: 74326

Gnomad4 AFR AF: 0.0461

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.000970

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.185

Alfa AF: 0.235 Hom.: 2124

Bravo AF: 0.163

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4772972; hg19: chr13-109110414;