rs13230419

chr7-80679969-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.380

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.5
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

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