rs1340900

Variant names:

• chr13-75043482-G-A
• rs1340900

Your query was ambiguous. Multiple possible variants found:

• chr13-75043482-G-A
• chr13-75043482-G-C
• chr13-75043482-G-T

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 0.478 in 151,254 control chromosomes in the GnomAD database, including 19,054 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 0.48 (19054 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.478 AC: 72270 AN: 151138 Hom.: 19051 Cov.: 30

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.478 AC: 72281 AN: 151254 Hom.: 19054 Cov.: 30 AF XY: 0.477 AC XY: 35249 AN XY: 73884

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.511

Alfa AF: 0.514 Hom.: 3516

Bravo AF: 0.468

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1340900; hg19: chr13-75617619;