chr13-97875612-G-A

Variant names:

• chr13-97875612-G-A
• rs7987913

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.707

Alfa AF: 0.727 Hom.: 25946

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7987913; hg19: chr13-98527866;