rs189811

Variant names:

• chr4-131961706-T-A
• rs189811
• ENST00000510592.1:n.30+14217A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-131961706-T-A
• chr4-131961706-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510592.1(ENSG00000251555):​n.30+14217A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,382 control chromosomes in the GnomAD database, including 33,952 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 0.66 (33952 hom., cov: 29)
• Consequence: ENSG00000251555 ENST00000510592.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

ENSG00000251555 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 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
ENSG00000251555	ENST00000510592.1	n.30+14217A>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.660 AC: 99763 AN: 151270 Hom.: 33937 Cov.: 29

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.659 AC: 99826 AN: 151382 Hom.: 33952 Cov.: 29 AF XY: 0.660 AC XY: 48816 AN XY: 73940

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.680

Alfa AF: 0.714 Hom.: 4789

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.073

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs189811; hg19: chr4-132882861;