rs1331519

Variant names:

• chr13-103693782-A-G
• rs1331519

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 0.193 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0973 AC: 4041 AN: 41542

American (AMR) AF: 0.132 AC: 2020 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3466

East Asian (EAS) AF: 0.197 AC: 1020 AN: 5178

South Asian (SAS) AF: 0.198 AC: 954 AN: 4814

European-Finnish (FIN) AF: 0.347 AC: 3658 AN: 10548

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16534 AN: 67992

Other (OTH) AF: 0.168 AC: 354 AN: 2106

Alfa AF: 0.228 Hom.: 11141

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1331519; hg19: chr13-104346132;