rs7333079

Variant names:

• chr13-60576777-A-T
• rs7333079

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;