rs1370072

Variant names:

• chr13-55267803-C-T
• rs1370072

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;