rs7333079

Variant names:

• chr13-60576777-A-T
• rs7333079
• ENST00000752837.1:n.158-3443T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000752837.1(ENSG00000298072):​n.158-3443T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000298072 ENST00000752837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 1 publications found

Genes affected

ENSG00000298072 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000298072	ENST00000752837.1	n.158-3443T>A		intron_variant	Intron 1 of 2
ENSG00000298072	ENST00000752838.1	n.161-3443T>A		intron_variant	Intron 1 of 2
ENSG00000298072	ENST00000752839.1	n.160-3443T>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.130 AC: 5381 AN: 41538

American (AMR) AF: 0.0453 AC: 693 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3470

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5188

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4824

European-Finnish (FIN) AF: 0.0374 AC: 397 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0620 AC: 4216 AN: 68024

Other (OTH) AF: 0.0720 AC: 152 AN: 2110

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
PhyloP100		0.086

Splicing

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

Other links and lift over

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