rs7996198

Variant names:

• chr13-59415033-T-C
• rs7996198

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 0.177 in 152,186 control chromosomes in the GnomAD database, including 2,494 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 0.18 (2494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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: 0.177 AC: 26961 AN: 152068 Hom.: 2492 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.177 AC: 26984 AN: 152186 Hom.: 2494 Cov.: 32 AF XY: 0.176 AC XY: 13084 AN XY: 74412

African (AFR) AF: 0.166 AC: 6907 AN: 41526

American (AMR) AF: 0.178 AC: 2715 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3468

East Asian (EAS) AF: 0.0411 AC: 213 AN: 5188

South Asian (SAS) AF: 0.159 AC: 768 AN: 4824

European-Finnish (FIN) AF: 0.153 AC: 1617 AN: 10600

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13412 AN: 67996

Other (OTH) AF: 0.179 AC: 378 AN: 2116

Alfa AF: 0.190 Hom.: 8452

Bravo AF: 0.177

Asia WGS AF: 0.104 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.9
DANN	Benign	0.65
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs7996198; hg19: chr13-59989167;