rs13232179

Variant names:

• chr7-151423862-T-A
• rs13232179

Your query was ambiguous. Multiple possible variants found:

• chr7-151423862-T-A
• chr7-151423862-T-C
• chr7-151423862-T-G

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 0.139 in 152,104 control chromosomes in the GnomAD database, including 2,106 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 0.14 (2106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 14 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 = 0.49 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: 0.139 AC: 21055 AN: 151986 Hom.: 2103 Cov.: 32

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.139 AC: 21073 AN: 152104 Hom.: 2106 Cov.: 32 AF XY: 0.145 AC XY: 10746 AN XY: 74366

African (AFR) AF: 0.0969 AC: 4018 AN: 41466

American (AMR) AF: 0.121 AC: 1853 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2619 AN: 5174

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4814

European-Finnish (FIN) AF: 0.0779 AC: 825 AN: 10592

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8737 AN: 67984

Other (OTH) AF: 0.152 AC: 321 AN: 2112

Alfa AF: 0.144 Hom.: 1076

Bravo AF: 0.139

Asia WGS AF: 0.360 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.79
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs13232179; hg19: chr7-151120948;