ENST00000510419.1:n.484-1238T>C

Variant names:

• chr4-74554070-A-G
• rs10034692
• ENST00000510419.1:n.484-1238T>C

Variant summary

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

The ENST00000510419.1(ENSG00000249942):​n.484-1238T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,060 control chromosomes in the GnomAD database, including 6,888 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 (6888 hom., cov: 32)
• Consequence: ENSG00000249942 ENST00000510419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 12 publications found

Genes affected

ENSG00000249942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986229	XR_001741513.2	n.174-1238T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249942	ENST00000510419.1	n.484-1238T>C		intron_variant	Intron 5 of 5	5
ENSG00000249942	ENST00000840127.1	n.419-1238T>C		intron_variant	Intron 5 of 5
ENSG00000249942	ENST00000840128.1	n.311-1238T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45173 AN: 151942 Hom.: 6888 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.297 AC: 45205 AN: 152060 Hom.: 6888 Cov.: 32 AF XY: 0.306 AC XY: 22734 AN XY: 74320

African (AFR) AF: 0.295 AC: 12249 AN: 41510

American (AMR) AF: 0.314 AC: 4792 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1618 AN: 5166

South Asian (SAS) AF: 0.342 AC: 1650 AN: 4822

European-Finnish (FIN) AF: 0.399 AC: 4211 AN: 10564

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18904 AN: 67956

Other (OTH) AF: 0.287 AC: 607 AN: 2112

Alfa AF: 0.288 Hom.: 14662

Bravo AF: 0.291

Asia WGS AF: 0.373 AC: 1294 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.61
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10034692; hg19: chr4-75419787;