rs7995376

Positions:

• chr13-108130707-C-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 0.0926 in 152,138 control chromosomes in the GnomAD database, including 1,292 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 0.093 (1292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14040 AN: 152020 Hom.: 1283 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0358

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0349

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0926 AC: 14083 AN: 152138 Hom.: 1292 Cov.: 32 AF XY: 0.0918 AC XY: 6830 AN XY: 74386

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.0580

Gnomad4 ASJ AF: 0.0358

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.0344

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0264

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0656 Hom.: 131

Bravo AF: 0.103

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7995376; hg19: chr13-108783055;