rs11741889

Variant names:

• chr5-135904273-A-T
• rs11741889
• ENST00000523722.1:n.598-3747T>A

Variant summary

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

The ENST00000523722.1(ENSG00000253927):​n.598-3747T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,038 control chromosomes in the GnomAD database, including 7,105 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 0.30 (7105 hom., cov: 32)
• Consequence: ENSG00000253927 ENST00000523722.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 2 publications found

Genes affected

ENSG00000253927 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523722.1. 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
	ENSG00000253927	ENST00000523722.1	TSL:3	n.598-3747T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45830 AN: 151920 Hom.: 7096 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.302 AC: 45864 AN: 152038 Hom.: 7105 Cov.: 32 AF XY: 0.298 AC XY: 22164 AN XY: 74318

African (AFR) AF: 0.272 AC: 11289 AN: 41494

American (AMR) AF: 0.269 AC: 4116 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5178

South Asian (SAS) AF: 0.323 AC: 1553 AN: 4808

European-Finnish (FIN) AF: 0.276 AC: 2910 AN: 10550

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21991 AN: 67956

Other (OTH) AF: 0.314 AC: 662 AN: 2106

Alfa AF: 0.316 Hom.: 962

Bravo AF: 0.298

Asia WGS AF: 0.286 AC: 1000 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	1.1
DANN	Benign	0.75
PhyloP100		-0.49

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: rs11741889;

hg19: chr5-135239962;