rs892535

Variant names:

• chr13-104557564-C-G
• rs892535

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.41 in 152,012 control chromosomes in the GnomAD database, including 14,445 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 0.41 (14445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 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: 0.410 AC: 62330 AN: 151894 Hom.: 14431 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.410 AC: 62378 AN: 152012 Hom.: 14445 Cov.: 32 AF XY: 0.399 AC XY: 29678 AN XY: 74300

African (AFR) AF: 0.621 AC: 25762 AN: 41460

American (AMR) AF: 0.299 AC: 4570 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1452 AN: 3468

East Asian (EAS) AF: 0.122 AC: 631 AN: 5174

South Asian (SAS) AF: 0.284 AC: 1369 AN: 4820

European-Finnish (FIN) AF: 0.236 AC: 2485 AN: 10544

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24728 AN: 67952

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.388 Hom.: 1559

Bravo AF: 0.424

Asia WGS AF: 0.202 AC: 704 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.24
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs892535; hg19: chr13-105209915;