4-23347368-C-A

Variant names:

• chr4-23347368-C-A
• rs2940775
• ENST00000757640.1:n.285-17925G>T

Variant summary

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

The ENST00000757640.1(ENSG00000298732):​n.285-17925G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 151,872 control chromosomes in the GnomAD database, including 48,173 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 0.79 (48173 hom., cov: 30)
• Consequence: ENSG00000298732 ENST00000757640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 2 publications found

Genes affected

ENSG00000298732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374523	XR_001741614.1	n.227-17925G>T		intron_variant	Intron 1 of 2
LOC105374524	XR_007058437.1	n.2932+13842C>A		intron_variant	Intron 16 of 18
LOC105374523	XR_925460.2	n.227-17925G>T		intron_variant	Intron 1 of 2
LOC105374523	XR_925461.2	n.266-17925G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298732	ENST00000757640.1	n.285-17925G>T		intron_variant	Intron 1 of 4
ENSG00000298732	ENST00000757641.1	n.268-17925G>T		intron_variant	Intron 1 of 3
ENSG00000298732	ENST00000757642.1	n.253-17925G>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120602 AN: 151754 Hom.: 48126 Cov.: 30

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.795 AC: 120709 AN: 151872 Hom.: 48173 Cov.: 30 AF XY: 0.799 AC XY: 59312 AN XY: 74248

African (AFR) AF: 0.823 AC: 34117 AN: 41438

American (AMR) AF: 0.854 AC: 13030 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2852 AN: 3466

East Asian (EAS) AF: 0.997 AC: 5116 AN: 5130

South Asian (SAS) AF: 0.841 AC: 4039 AN: 4804

European-Finnish (FIN) AF: 0.792 AC: 8373 AN: 10570

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50550 AN: 67892

Other (OTH) AF: 0.806 AC: 1703 AN: 2112

Alfa AF: 0.757 Hom.: 9090

Bravo AF: 0.805

Asia WGS AF: 0.911 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.39
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs2940775; hg19: chr4-23348991;