rs1375749

Variant names:

• chr4-176540214-A-G
• rs1375749
• ENST00000752489.1:n.282+19800A>G

Variant summary

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

The ENST00000752489.1(ENSG00000298014):​n.282+19800A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,280 control chromosomes in the GnomAD database, including 5,300 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 0.24 (5300 hom., cov: 29)
• Consequence: ENSG00000298014 ENST00000752489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 3 publications found

Genes affected

ENSG00000298014 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 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
ENSG00000298014	ENST00000752489.1	n.282+19800A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36383 AN: 151160 Hom.: 5294 Cov.: 29

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0914

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.241 AC: 36397 AN: 151280 Hom.: 5300 Cov.: 29 AF XY: 0.239 AC XY: 17636 AN XY: 73916

African (AFR) AF: 0.0954 AC: 3940 AN: 41296

American (AMR) AF: 0.244 AC: 3710 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3470

East Asian (EAS) AF: 0.0916 AC: 461 AN: 5034

South Asian (SAS) AF: 0.142 AC: 671 AN: 4742

European-Finnish (FIN) AF: 0.316 AC: 3277 AN: 10386

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21852 AN: 67840

Other (OTH) AF: 0.240 AC: 504 AN: 2100

Alfa AF: 0.292 Hom.: 8716

Bravo AF: 0.231

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.71
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1375749; hg19: chr4-177461365;