rs4240241

Variant names:

• chr4-37765310-G-A
• rs4240241
• ENST00000842454.1:n.445+2458G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-37765310-G-A
• chr4-37765310-G-C
• chr4-37765310-G-T

Variant summary

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

The ENST00000842454.1(ENSG00000309616):​n.445+2458G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,206 control chromosomes in the GnomAD database, including 58,895 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 0.87 (58895 hom., cov: 32)
• Consequence: ENSG00000309616 ENST00000842454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 2 publications found

Genes affected

ENSG00000309616 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.952 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
ENSG00000309616	ENST00000842454.1	n.445+2458G>A		intron_variant	Intron 3 of 3
ENSG00000309616	ENST00000842455.1	n.357+2458G>A		intron_variant	Intron 3 of 4
ENSG00000309616	ENST00000842456.1	n.343+2458G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132644 AN: 152088 Hom.: 58886 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.872 AC: 132693 AN: 152206 Hom.: 58895 Cov.: 32 AF XY: 0.873 AC XY: 64952 AN XY: 74424

African (AFR) AF: 0.687 AC: 28496 AN: 41456

American (AMR) AF: 0.872 AC: 13338 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3374 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4620 AN: 5186

South Asian (SAS) AF: 0.885 AC: 4264 AN: 4820

European-Finnish (FIN) AF: 0.978 AC: 10375 AN: 10606

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65189 AN: 68044

Other (OTH) AF: 0.879 AC: 1859 AN: 2116

Alfa AF: 0.924 Hom.: 210824

Bravo AF: 0.856

Asia WGS AF: 0.861 AC: 2995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.18
DANN	Benign	0.54
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs4240241; hg19: chr4-37766932;