rs1330047

Variant names:

• chr13-85942869-G-A
• rs1330047

Your query was ambiguous. Multiple possible variants found:

• chr13-85942869-G-A
• chr13-85942869-G-C

Variant summary

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

The variant allele was found at a frequency of 0.738 in 152,028 control chromosomes in the GnomAD database, including 41,469 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 0.74 (41469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 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: 0.738 AC: 112172 AN: 151910 Hom.: 41438 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.738 AC: 112246 AN: 152028 Hom.: 41469 Cov.: 32 AF XY: 0.738 AC XY: 54846 AN XY: 74300

African (AFR) AF: 0.721 AC: 29919 AN: 41484

American (AMR) AF: 0.746 AC: 11370 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2132 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3621 AN: 5154

South Asian (SAS) AF: 0.650 AC: 3127 AN: 4810

European-Finnish (FIN) AF: 0.770 AC: 8141 AN: 10572

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.758 AC: 51511 AN: 67968

Other (OTH) AF: 0.729 AC: 1543 AN: 2116

Alfa AF: 0.738 Hom.: 16388

Bravo AF: 0.734

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.058
DANN	Benign	0.53
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1330047; hg19: chr13-86517004;