rs7987913

Positions:

• chr13-97875612-G-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.97875612G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;