rs13223346

Variant names:

• chr7-141792710-A-G
• rs13223346

Your query was ambiguous. Multiple possible variants found:

• chr7-141792710-A-G
• chr7-141792710-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 0.426 in 152,116 control chromosomes in the GnomAD database, including 14,727 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 0.43 (14727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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: 0.426 AC: 64794 AN: 151998 Hom.: 14719 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.426 AC: 64833 AN: 152116 Hom.: 14727 Cov.: 33 AF XY: 0.429 AC XY: 31890 AN XY: 74376

African (AFR) AF: 0.248 AC: 10293 AN: 41516

American (AMR) AF: 0.495 AC: 7573 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3466

East Asian (EAS) AF: 0.691 AC: 3570 AN: 5170

South Asian (SAS) AF: 0.441 AC: 2128 AN: 4826

European-Finnish (FIN) AF: 0.462 AC: 4884 AN: 10572

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33431 AN: 67968

Other (OTH) AF: 0.458 AC: 967 AN: 2110

Alfa AF: 0.344 Hom.: 1329

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs13223346; hg19: chr7-141492510;