chr13-21255170-G-T

Variant names:

• chr13-21255170-G-T
• rs9316212

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 0.158 in 152,174 control chromosomes in the GnomAD database, including 2,264 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 0.16 (2264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 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: 0.158 AC: 24018 AN: 152056 Hom.: 2263 Cov.: 32

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.00675

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.158 AC: 24022 AN: 152174 Hom.: 2264 Cov.: 32 AF XY: 0.156 AC XY: 11576 AN XY: 74384

African (AFR) AF: 0.0726 AC: 3018 AN: 41544

American (AMR) AF: 0.140 AC: 2133 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.00676 AC: 35 AN: 5176

South Asian (SAS) AF: 0.146 AC: 704 AN: 4824

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10572

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14566 AN: 67986

Other (OTH) AF: 0.173 AC: 366 AN: 2110

Alfa AF: 0.195 Hom.: 9688

Bravo AF: 0.150

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	-0.92
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs9316212; hg19: chr13-21829309;