19-20576902-A-T

Variant names:

• chr19-20576902-A-T
• rs7259082
• ENST00000595094.1:n.478+3305T>A

Variant summary

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

The ENST00000595094.1(ENSG00000269110):​n.478+3305T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 148,852 control chromosomes in the GnomAD database, including 41,883 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 0.75 (41883 hom., cov: 25)
• Consequence: ENSG00000269110 ENST00000595094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ENSG00000269110 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.767 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
ENSG00000269110	ENST00000595094.1	n.478+3305T>A		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.749 AC: 111437 AN: 148734 Hom.: 41866 Cov.: 25

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.798

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.749 AC: 111501 AN: 148852 Hom.: 41883 Cov.: 25 AF XY: 0.746 AC XY: 54054 AN XY: 72506

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.766

Alfa AF: 0.593 Hom.: 1121

Asia WGS AF: 0.734 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7259082; hg19: chr19-20759708;