rs2772175

Variant names:

• chr13-20726573-T-A
• rs2772175

Your query was ambiguous. Multiple possible variants found:

• chr13-20726573-T-A
• chr13-20726573-T-G

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 0.45 in 152,124 control chromosomes in the GnomAD database, including 17,201 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 0.45 (17201 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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: 0.449 AC: 68315 AN: 152008 Hom.: 17161 Cov.: 33

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.450 AC: 68413 AN: 152124 Hom.: 17201 Cov.: 33 AF XY: 0.460 AC XY: 34219 AN XY: 74366

African (AFR) AF: 0.608 AC: 25214 AN: 41504

American (AMR) AF: 0.527 AC: 8052 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3468

East Asian (EAS) AF: 0.758 AC: 3916 AN: 5168

South Asian (SAS) AF: 0.633 AC: 3055 AN: 4824

European-Finnish (FIN) AF: 0.397 AC: 4199 AN: 10582

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21907 AN: 67968

Other (OTH) AF: 0.399 AC: 844 AN: 2114

Alfa AF: 0.265 Hom.: 632

Bravo AF: 0.462

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.71
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2772175; hg19: chr13-21300712;