rs7997100

Variant names:

• chr13-68515942-C-T
• rs7997100

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 0.273 in 151,886 control chromosomes in the GnomAD database, including 5,853 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 0.27 (5853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 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: 0.273 AC: 41383 AN: 151770 Hom.: 5841 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.273 AC: 41443 AN: 151886 Hom.: 5853 Cov.: 32 AF XY: 0.270 AC XY: 20080 AN XY: 74246

African (AFR) AF: 0.276 AC: 11424 AN: 41418

American (AMR) AF: 0.344 AC: 5234 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3466

East Asian (EAS) AF: 0.163 AC: 841 AN: 5172

South Asian (SAS) AF: 0.263 AC: 1268 AN: 4822

European-Finnish (FIN) AF: 0.183 AC: 1938 AN: 10570

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18046 AN: 67902

Other (OTH) AF: 0.313 AC: 661 AN: 2110

Alfa AF: 0.273 Hom.: 3066

Bravo AF: 0.286

Asia WGS AF: 0.239 AC: 833 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	0.050
DANN	Benign	0.40
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7997100; hg19: chr13-69090074;