rs4234840

Variant names:

• chr4-4915784-A-G
• rs4234840
• ENST00000834472.1:n.97-1126T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-4915784-A-G
• chr4-4915784-A-T

Variant summary

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

The ENST00000834472.1(ENSG00000308474):​n.97-1126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,004 control chromosomes in the GnomAD database, including 39,786 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 0.72 (39786 hom., cov: 31)
• Consequence: ENSG00000308474 ENST00000834472.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 4 publications found

Genes affected

ENSG00000308474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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
ENSG00000308474	ENST00000834472.1	n.97-1126T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109524 AN: 151884 Hom.: 39748 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.721 AC: 109623 AN: 152004 Hom.: 39786 Cov.: 31 AF XY: 0.731 AC XY: 54311 AN XY: 74302

African (AFR) AF: 0.725 AC: 30046 AN: 41430

American (AMR) AF: 0.790 AC: 12088 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2452 AN: 3468

East Asian (EAS) AF: 0.902 AC: 4653 AN: 5156

South Asian (SAS) AF: 0.832 AC: 4009 AN: 4818

European-Finnish (FIN) AF: 0.763 AC: 8080 AN: 10596

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.678 AC: 46051 AN: 67932

Other (OTH) AF: 0.726 AC: 1531 AN: 2110

Alfa AF: 0.700 Hom.: 31032

Bravo AF: 0.720

Asia WGS AF: 0.840 AC: 2922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.54
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4234840; hg19: chr4-4917511;