chr13-97875612-G-A

Variant names:

• chr13-97875612-G-A
• rs7987913

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 0.668 in 152,124 control chromosomes in the GnomAD database, including 34,568 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 0.67 (34568 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 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: 0.668 AC: 101534 AN: 152006 Hom.: 34548 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.668 AC: 101591 AN: 152124 Hom.: 34568 Cov.: 33 AF XY: 0.662 AC XY: 49204 AN XY: 74368

African (AFR) AF: 0.595 AC: 24679 AN: 41480

American (AMR) AF: 0.603 AC: 9216 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2799 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2144 AN: 5176

South Asian (SAS) AF: 0.689 AC: 3326 AN: 4826

European-Finnish (FIN) AF: 0.650 AC: 6875 AN: 10572

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50096 AN: 67990

Other (OTH) AF: 0.707 AC: 1494 AN: 2112

Alfa AF: 0.716 Hom.: 81108

Bravo AF: 0.658

Asia WGS AF: 0.579 AC: 2014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.17
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7987913; hg19: chr13-98527866;