ENST00000503037.3:n.245-3907T>A

Variant names:

• chr4-187000345-A-T
• rs7660345
• ENST00000503037.3:n.245-3907T>A

Variant summary

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

The ENST00000503037.3(ENSG00000249742):​n.245-3907T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,044 control chromosomes in the GnomAD database, including 15,447 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 0.42 (15447 hom., cov: 33)
• Consequence: ENSG00000249742 ENST00000503037.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 3 publications found

Genes affected

ENSG00000249742 (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 (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723906	XR_002959826.2	n.329-19476A>T		intron_variant	Intron 1 of 3
LOC102723906	XR_007058501.1	n.329-19476A>T		intron_variant	Intron 1 of 2
LOC102723906	XR_007058502.1	n.329-19476A>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249742	ENST00000503037.3	n.245-3907T>A		intron_variant	Intron 2 of 3	3
ENSG00000250971	ENST00000839407.1	n.396-19476A>T		intron_variant	Intron 1 of 6
ENSG00000250971	ENST00000839408.1	n.186-19476A>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63083 AN: 151926 Hom.: 15410 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.415 AC: 63173 AN: 152044 Hom.: 15447 Cov.: 33 AF XY: 0.412 AC XY: 30641 AN XY: 74330

African (AFR) AF: 0.692 AC: 28673 AN: 41460

American (AMR) AF: 0.381 AC: 5831 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1813 AN: 5156

South Asian (SAS) AF: 0.416 AC: 2003 AN: 4818

European-Finnish (FIN) AF: 0.220 AC: 2321 AN: 10566

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20492 AN: 67966

Other (OTH) AF: 0.388 AC: 822 AN: 2116

Alfa AF: 0.354 Hom.: 1384

Bravo AF: 0.436

Asia WGS AF: 0.385 AC: 1336 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	8.7
DANN	Benign	0.73
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs7660345; hg19: chr4-187921499;