rs9521445

Variant names:

• chr13-109633187-C-A
• rs9521445
• ENST00000650264.1:n.759-62029G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-109633187-C-A
• chr13-109633187-C-T

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-62029G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,964 control chromosomes in the GnomAD database, including 15,783 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 0.45 (15783 hom., cov: 32)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 9 publications found

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650264.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285534	ENST00000650264.1		n.759-62029G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68196 AN: 151846 Hom.: 15776 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.449 AC: 68232 AN: 151964 Hom.: 15783 Cov.: 32 AF XY: 0.442 AC XY: 32842 AN XY: 74254

African (AFR) AF: 0.359 AC: 14866 AN: 41434

American (AMR) AF: 0.345 AC: 5269 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1872 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1848 AN: 5148

South Asian (SAS) AF: 0.360 AC: 1739 AN: 4826

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10542

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35507 AN: 67976

Other (OTH) AF: 0.464 AC: 976 AN: 2104

Alfa AF: 0.387 Hom.: 1797

Bravo AF: 0.434

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.55
PhyloP100		0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9521445;

hg19: chr13-110285534;