ENST00000734076.1:n.299-10754G>T

Variant names:

• chr4-3978411-C-A
• rs4974767
• ENST00000734076.1:n.299-10754G>T

Variant summary

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

The ENST00000734076.1(ENSG00000290888):​n.299-10754G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,988 control chromosomes in the GnomAD database, including 9,703 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 0.34 (9703 hom., cov: 32)
• Consequence: ENSG00000290888 ENST00000734076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 3 publications found

Genes affected

ENSG00000290888 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 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
ENSG00000290888	ENST00000734076.1	n.299-10754G>T		intron_variant	Intron 1 of 2
ENSG00000295948	ENST00000734305.1	n.273+14484C>A		intron_variant	Intron 2 of 3
ENSG00000295948	ENST00000734306.1	n.310+38100C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51306 AN: 151870 Hom.: 9704 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.338 AC: 51312 AN: 151988 Hom.: 9703 Cov.: 32 AF XY: 0.332 AC XY: 24688 AN XY: 74300

African (AFR) AF: 0.209 AC: 8660 AN: 41418

American (AMR) AF: 0.439 AC: 6708 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3470

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5180

South Asian (SAS) AF: 0.191 AC: 919 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3572 AN: 10554

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28382 AN: 67976

Other (OTH) AF: 0.398 AC: 837 AN: 2104

Alfa AF: 0.395 Hom.: 53777

Bravo AF: 0.341

Asia WGS AF: 0.124 AC: 432 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs4974767; hg19: chr4-3980138;