ENST00000787024.1:n.97-17174G>A

Variant names:

• chr11-18047874-G-A
• rs4757610
• ENST00000787024.1:n.97-17174G>A

Variant summary

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

The ENST00000787024.1(ENSG00000302464):​n.97-17174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,962 control chromosomes in the GnomAD database, including 14,796 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 0.43 (14796 hom., cov: 32)
• Consequence: ENSG00000302464 ENST00000787024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66
• Publications: 2 publications found

Genes affected

ENSG00000302464 (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 = 0.532 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
ENSG00000302464	ENST00000787024.1	n.97-17174G>A		intron_variant	Intron 1 of 1
ENSG00000302464	ENST00000787025.1	n.98-14064G>A		intron_variant	Intron 1 of 2
ENSG00000302464	ENST00000787026.1	n.94-14064G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65718 AN: 151844 Hom.: 14781 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.433 AC: 65784 AN: 151962 Hom.: 14796 Cov.: 32 AF XY: 0.425 AC XY: 31574 AN XY: 74274

African (AFR) AF: 0.538 AC: 22286 AN: 41456

American (AMR) AF: 0.357 AC: 5451 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1163 AN: 5184

South Asian (SAS) AF: 0.342 AC: 1647 AN: 4818

European-Finnish (FIN) AF: 0.386 AC: 4065 AN: 10518

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28627 AN: 67926

Other (OTH) AF: 0.436 AC: 922 AN: 2116

Alfa AF: 0.421 Hom.: 1727

Bravo AF: 0.436

Asia WGS AF: 0.306 AC: 1069 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs4757610; hg19: chr11-18069421;