rs1538001

Variant names:

• chr13-34210931-G-A
• rs1538001

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 0.747 in 152,056 control chromosomes in the GnomAD database, including 42,695 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 0.75 (42695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 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: 0.748 AC: 113579 AN: 151940 Hom.: 42679 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.747 AC: 113634 AN: 152056 Hom.: 42695 Cov.: 32 AF XY: 0.744 AC XY: 55276 AN XY: 74322

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.765

Alfa AF: 0.767 Hom.: 19360

Bravo AF: 0.738

Asia WGS AF: 0.705 AC: 2449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	16
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1538001; hg19: chr13-34785068;