19-7739434-A-T

Variant names:

• chr19-7739434-A-T
• rs8112310
• ENST00000678003.1:n.*290+2133T>A

Variant summary

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

The ENST00000678003.1(ENSG00000288669):​n.*290+2133T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,942 control chromosomes in the GnomAD database, including 41,661 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 0.71 (41661 hom., cov: 30)
• Consequence: ENSG00000288669 ENST00000678003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 6 publications found

Genes affected

ENSG00000288669 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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
ENSG00000288669	ENST00000678003.1	n.*290+2133T>A		intron_variant	Intron 2 of 12			ENSP00000504497.1
ENSG00000288669	ENST00000676543.1	n.71-5460T>A		intron_variant	Intron 1 of 11			ENSP00000503143.1
ENSG00000288669	ENST00000678227.1	n.579+2133T>A		intron_variant	Intron 1 of 1
ENSG00000288669	ENST00000678780.1	n.*1794+2133T>A		intron_variant	Intron 4 of 12			ENSP00000503751.1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108445 AN: 151824 Hom.: 41645 Cov.: 30

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.714 AC: 108492 AN: 151942 Hom.: 41661 Cov.: 30 AF XY: 0.716 AC XY: 53165 AN XY: 74246

African (AFR) AF: 0.401 AC: 16600 AN: 41426

American (AMR) AF: 0.801 AC: 12233 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2924 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3434 AN: 5112

South Asian (SAS) AF: 0.789 AC: 3801 AN: 4818

European-Finnish (FIN) AF: 0.878 AC: 9292 AN: 10588

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57647 AN: 67950

Other (OTH) AF: 0.758 AC: 1597 AN: 2108

Alfa AF: 0.771 Hom.: 5605

Bravo AF: 0.695

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.23
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs8112310; hg19: chr19-7804320;