rs7995376

Variant names:

• chr13-108130707-C-A
• rs7995376

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 0.0926 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.245 AC: 10139 AN: 41446

American (AMR) AF: 0.0580 AC: 886 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0358 AC: 124 AN: 3468

East Asian (EAS) AF: 0.118 AC: 611 AN: 5164

South Asian (SAS) AF: 0.0344 AC: 166 AN: 4832

European-Finnish (FIN) AF: 0.0160 AC: 170 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0264 AC: 1795 AN: 68008

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.0715 Hom.: 161

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
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs7995376; hg19: chr13-108783055;