rs4772972

Variant names:

• chr13-108458066-C-T
• rs4772972

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 0.175 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0461 AC: 1914 AN: 41522

American (AMR) AF: 0.151 AC: 2308 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3462

East Asian (EAS) AF: 0.000970 AC: 5 AN: 5156

South Asian (SAS) AF: 0.179 AC: 862 AN: 4824

European-Finnish (FIN) AF: 0.218 AC: 2302 AN: 10560

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17633 AN: 67948

Other (OTH) AF: 0.185 AC: 391 AN: 2114

Alfa AF: 0.236 Hom.: 2367

Bravo AF: 0.163

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.92
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4772972; hg19: chr13-109110414;