rs7990319

Variant names:

• chr13-55222716-A-G
• rs7990319

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 0.337 in 151,844 control chromosomes in the GnomAD database, including 10,409 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 0.34 (10409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.337 AC: 51122 AN: 151726 Hom.: 10416 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.337 AC: 51107 AN: 151844 Hom.: 10409 Cov.: 32 AF XY: 0.339 AC XY: 25132 AN XY: 74198

African (AFR) AF: 0.113 AC: 4677 AN: 41480

American (AMR) AF: 0.357 AC: 5419 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3468

East Asian (EAS) AF: 0.275 AC: 1418 AN: 5156

South Asian (SAS) AF: 0.272 AC: 1314 AN: 4828

European-Finnish (FIN) AF: 0.521 AC: 5491 AN: 10540

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30243 AN: 67864

Other (OTH) AF: 0.344 AC: 725 AN: 2110

Alfa AF: 0.398 Hom.: 6835

Bravo AF: 0.317

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.8
DANN	Benign	0.58
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs7990319; hg19: chr13-55796851; COSMIC: COSV69351502;