rs4739466

Variant names:

• chr8-37084024-G-T
• rs4739466
• ENST00000744926.1:n.223-7912C>A

Variant summary

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

The ENST00000744926.1(ENSG00000297043):​n.223-7912C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,156 control chromosomes in the GnomAD database, including 1,005 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 0.11 (1005 hom., cov: 33)
• Consequence: ENSG00000297043 ENST00000744926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641
• Publications: 4 publications found

Genes affected

ENSG00000297043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 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
ENSG00000297043	ENST00000744926.1	n.223-7912C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16314 AN: 152038 Hom.: 1001 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.107 AC: 16326 AN: 152156 Hom.: 1005 Cov.: 33 AF XY: 0.110 AC XY: 8190 AN XY: 74394

African (AFR) AF: 0.110 AC: 4564 AN: 41522

American (AMR) AF: 0.138 AC: 2105 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1329 AN: 5180

South Asian (SAS) AF: 0.107 AC: 515 AN: 4826

European-Finnish (FIN) AF: 0.128 AC: 1349 AN: 10570

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0862 AC: 5859 AN: 67990

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.0955 Hom.: 1340

Bravo AF: 0.111

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.56
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs4739466; hg19: chr8-36941542;