rs13223346

chr7-141792710-A-Gchr7-141792710-A-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 0.426 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.458

Alfa AF: 0.349 Hom.: 1310

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13223346; hg19: chr7-141492510;