rs1340169

Variant names:

• chr13-72403923-T-G
• rs1340169

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0326 in 152,214 control chromosomes in the GnomAD database, including 240 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 0.033 (240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.96

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.134 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: 0.0325 AC: 4942 AN: 152096 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.00763

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0326 AC: 4961 AN: 152214 Hom.: 240 Cov.: 32 AF XY: 0.0342 AC XY: 2545 AN XY: 74430

Gnomad4 AFR AF: 0.00765

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0191

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0285

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0310 Hom.: 34

Bravo AF: 0.0427

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	19
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1340169; hg19: chr13-72978061;