ENST00000743803.1:n.235+11757T>C

Variant names:

• chr4-35370476-T-C
• rs437943
• ENST00000743803.1:n.235+11757T>C

Variant summary

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

The ENST00000743803.1(ENSG00000296945):​n.235+11757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,092 control chromosomes in the GnomAD database, including 18,980 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 0.46 (18980 hom., cov: 32)
• Consequence: ENSG00000296945 ENST00000743803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 16 publications found

Genes affected

ENSG00000296945 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 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
ENSG00000296945	ENST00000743803.1	n.235+11757T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70559 AN: 151972 Hom.: 18935 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.465 AC: 70663 AN: 152092 Hom.: 18980 Cov.: 32 AF XY: 0.461 AC XY: 34250 AN XY: 74350

African (AFR) AF: 0.749 AC: 31094 AN: 41502

American (AMR) AF: 0.428 AC: 6542 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.391 AC: 2018 AN: 5156

South Asian (SAS) AF: 0.310 AC: 1495 AN: 4828

European-Finnish (FIN) AF: 0.325 AC: 3440 AN: 10582

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23381 AN: 67964

Other (OTH) AF: 0.412 AC: 869 AN: 2108

Alfa AF: 0.381 Hom.: 51881

Bravo AF: 0.485

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs437943; hg19: chr4-35372098;