ENST00000519844.2:n.152+1165A>G

Variant names:

• chr8-100409570-T-C
• rs6994682
• ENST00000519844.2:n.152+1165A>G

Variant summary

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

The ENST00000519844.2(ENSG00000253824):​n.152+1165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,090 control chromosomes in the GnomAD database, including 12,802 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 0.30 (12802 hom., cov: 32)
• Consequence: ENSG00000253824 ENST00000519844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

ENSG00000253824 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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
ENSG00000253824	ENST00000519844.2	n.152+1165A>G		intron_variant	Intron 2 of 2	3
ENSG00000253824	ENST00000654832.1	n.180+4795A>G		intron_variant	Intron 1 of 1
ENSG00000253824	ENST00000657736.1	n.63+4795A>G		intron_variant	Intron 1 of 2
ENSG00000253824	ENST00000664475.1	n.120-27799A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45495 AN: 151972 Hom.: 12760 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.300 AC: 45591 AN: 152090 Hom.: 12802 Cov.: 32 AF XY: 0.294 AC XY: 21849 AN XY: 74344

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.256

Alfa AF: 0.149 Hom.: 4270

Bravo AF: 0.325

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.79

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

Publications

LitVar

Other links and lift over

dbSNP: rs6994682; hg19: chr8-101421798;