rs7333079

chr13-60576777-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 0.0766 in 152,262 control chromosomes in the GnomAD database, including 572 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 0.077 (572 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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: 0.0766 AC: 11655 AN: 152144 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0766 AC: 11662 AN: 152262 Hom.: 572 Cov.: 33 AF XY: 0.0739 AC XY: 5504 AN XY: 74452

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0453

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.0560

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0620

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.0655 Hom.: 51

Bravo AF: 0.0787

Asia WGS AF: 0.0570 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	8.0
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7333079; hg19: chr13-61150911; COSMIC: COSV52163243;