rs1330047

chr13-85942869-G-Achr13-85942869-G-C

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 0.738 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.729

Alfa AF: 0.737 Hom.: 14030

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330047; hg19: chr13-86517004;