rs1370072

chr13-55267803-C-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 0.34 in 151,920 control chromosomes in the GnomAD database, including 10,549 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 0.34 (10549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 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: 0.341 AC: 51721 AN: 151802 Hom.: 10551 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.340 AC: 51718 AN: 151920 Hom.: 10549 Cov.: 32 AF XY: 0.342 AC XY: 25382 AN XY: 74226

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.349

Alfa AF: 0.411 Hom.: 9731

Bravo AF: 0.322

Asia WGS AF: 0.246 AC: 855 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	15
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: rs1370072; hg19: chr13-55841938; COSMIC: COSV69351540;