rs189811

chr4-131961706-T-Achr4-131961706-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, non coding transcript 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: ENST00000510592.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000510592.1	n.30+14217A>T		intron_variant, non_coding_transcript_variant		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;