19-20576902-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000269110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595094.1. 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
	ENSG00000269110	ENST00000595094.1	TSL:5	n.478+3305T>A		intron	N/A

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

African (AFR) AF: 0.739 AC: 29973 AN: 40556

American (AMR) AF: 0.779 AC: 11599 AN: 14898

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2659 AN: 3420

East Asian (EAS) AF: 0.745 AC: 3766 AN: 5052

South Asian (SAS) AF: 0.666 AC: 3097 AN: 4652

European-Finnish (FIN) AF: 0.732 AC: 7431 AN: 10158

Middle Eastern (MID) AF: 0.810 AC: 235 AN: 290

European-Non Finnish (NFE) AF: 0.754 AC: 50421 AN: 66872

Other (OTH) AF: 0.766 AC: 1576 AN: 2058

Alfa AF: 0.593 Hom.: 1121

Asia WGS AF: 0.734 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.5
DANN	Benign	0.26
PhyloP100		-1.0

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: rs7259082;

hg19: chr19-20759708;