rs13230419

Variant names:

• chr7-80679969-C-T
• rs13230419

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 0.356 in 151,944 control chromosomes in the GnomAD database, including 10,655 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 0.36 (10655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54037 AN: 151826 Hom.: 10650 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.356 AC: 54060 AN: 151944 Hom.: 10655 Cov.: 32 AF XY: 0.356 AC XY: 26450 AN XY: 74234

African (AFR) AF: 0.167 AC: 6942 AN: 41460

American (AMR) AF: 0.342 AC: 5208 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2256 AN: 5164

South Asian (SAS) AF: 0.436 AC: 2100 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4707 AN: 10538

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30066 AN: 67934

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.390 Hom.: 1505

Bravo AF: 0.337

Asia WGS AF: 0.445 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs13230419; hg19: chr7-80309285; COSMIC: COSV71705325;