19-8269396-C-T

Variant names:

• chr19-8269396-C-T
• rs250508
• ENST00000796540.1:n.854+24410G>A

Variant summary

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

The ENST00000796540.1(ENSG00000303688):​n.854+24410G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,160 control chromosomes in the GnomAD database, including 28,625 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 0.59 (28625 hom., cov: 33)
• Consequence: ENSG00000303688 ENST00000796540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 11 publications found

Genes affected

ENSG00000303688 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 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
ENSG00000303688	ENST00000796540.1	n.854+24410G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89454 AN: 152042 Hom.: 28583 Cov.: 33

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.589 AC: 89552 AN: 152160 Hom.: 28625 Cov.: 33 AF XY: 0.599 AC XY: 44555 AN XY: 74372

African (AFR) AF: 0.823 AC: 34177 AN: 41534

American (AMR) AF: 0.549 AC: 8392 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1681 AN: 3468

East Asian (EAS) AF: 0.785 AC: 4068 AN: 5184

South Asian (SAS) AF: 0.644 AC: 3104 AN: 4820

European-Finnish (FIN) AF: 0.587 AC: 6211 AN: 10588

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30062 AN: 67976

Other (OTH) AF: 0.550 AC: 1162 AN: 2112

Alfa AF: 0.487 Hom.: 84070

Bravo AF: 0.595

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.54
PhyloP100		-2.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs250508; hg19: chr19-8334280;