rs1538001

Variant names:

• chr13-34210931-G-A
• rs1538001

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.729 AC: 30235 AN: 41456

American (AMR) AF: 0.672 AC: 10274 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2800 AN: 3472

East Asian (EAS) AF: 0.741 AC: 3838 AN: 5180

South Asian (SAS) AF: 0.738 AC: 3557 AN: 4820

European-Finnish (FIN) AF: 0.747 AC: 7885 AN: 10552

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52565 AN: 67968

Other (OTH) AF: 0.765 AC: 1619 AN: 2116

Alfa AF: 0.766 Hom.: 21830

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
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1538001; hg19: chr13-34785068;