rs17073403

Variant names:

• chr13-21911760-G-A
• rs17073403

Your query was ambiguous. Multiple possible variants found:

• chr13-21911760-G-A
• chr13-21911760-G-C

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 0.274 in 152,134 control chromosomes in the GnomAD database, including 6,155 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 (6155 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.274 AC: 41634 AN: 152016 Hom.: 6137 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.274 AC: 41700 AN: 152134 Hom.: 6155 Cov.: 33 AF XY: 0.274 AC XY: 20383 AN XY: 74360

African (AFR) AF: 0.366 AC: 15194 AN: 41502

American (AMR) AF: 0.205 AC: 3143 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3468

East Asian (EAS) AF: 0.118 AC: 613 AN: 5182

South Asian (SAS) AF: 0.243 AC: 1173 AN: 4818

European-Finnish (FIN) AF: 0.333 AC: 3521 AN: 10570

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16394 AN: 67986

Other (OTH) AF: 0.266 AC: 561 AN: 2108

Alfa AF: 0.232 Hom.: 2305

Bravo AF: 0.267

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs17073403; hg19: chr13-22485899;