19-20951457-T-A

Variant names:

• chr19-20951457-T-A
• rs11672610
• ENST00000758057.1:n.278+19921A>T

Variant summary

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

The ENST00000758057.1(ENSG00000298806):​n.278+19921A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,244 control chromosomes in the GnomAD database, including 1,010 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 0.11 (1010 hom., cov: 32)
• Consequence: ENSG00000298806 ENST00000758057.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 5 publications found

Genes affected

ENSG00000298806 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 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
ENSG00000298806	ENST00000758057.1	n.278+19921A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17208 AN: 152126 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.0810

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.113 AC: 17214 AN: 152244 Hom.: 1010 Cov.: 32 AF XY: 0.112 AC XY: 8314 AN XY: 74436

African (AFR) AF: 0.104 AC: 4315 AN: 41540

American (AMR) AF: 0.0807 AC: 1235 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3472

East Asian (EAS) AF: 0.0308 AC: 160 AN: 5190

South Asian (SAS) AF: 0.118 AC: 570 AN: 4826

European-Finnish (FIN) AF: 0.121 AC: 1280 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8855 AN: 68008

Other (OTH) AF: 0.0912 AC: 193 AN: 2116

Alfa AF: 0.122 Hom.: 151

Bravo AF: 0.110

Asia WGS AF: 0.0880 AC: 308 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.20
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs11672610; hg19: chr19-21134263;