rs7990340

Variant names:

• chr13-34117703-A-G
• rs7990340

Your query was ambiguous. Multiple possible variants found:

• chr13-34117703-A-G
• chr13-34117703-A-T

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 0.328 in 152,096 control chromosomes in the GnomAD database, including 8,707 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 0.33 (8707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.856
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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: 0.328 AC: 49799 AN: 151978 Hom.: 8702 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.328 AC: 49832 AN: 152096 Hom.: 8707 Cov.: 32 AF XY: 0.330 AC XY: 24560 AN XY: 74338

African (AFR) AF: 0.399 AC: 16536 AN: 41456

American (AMR) AF: 0.325 AC: 4969 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3094 AN: 5154

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4822

European-Finnish (FIN) AF: 0.221 AC: 2340 AN: 10600

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18542 AN: 67992

Other (OTH) AF: 0.346 AC: 732 AN: 2116

Alfa AF: 0.294 Hom.: 19605

Bravo AF: 0.336

Asia WGS AF: 0.528 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.69
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs7990340; hg19: chr13-34691840;