rs1331519

Positions:

• chr13-103693782-A-G

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 0.193 in 152,140 control chromosomes in the GnomAD database, including 3,338 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 0.19 (3338 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29322 AN: 152022 Hom.: 3335 Cov.: 33

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.193 AC: 29334 AN: 152140 Hom.: 3338 Cov.: 33 AF XY: 0.194 AC XY: 14451 AN XY: 74368

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.168

Alfa AF: 0.229 Hom.: 4646

Bravo AF: 0.172

Asia WGS AF: 0.207 AC: 717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
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: rs1331519; hg19: chr13-104346132;