rs4659444

Variant names:

• chr1-26498625-C-T
• rs4659444
• ENST00000726050.1:n.719G>A

Variant summary

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

The ENST00000726050.1(ENSG00000294798):​n.719G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,958 control chromosomes in the GnomAD database, including 8,612 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 0.31 (8612 hom., cov: 31)
• Consequence: ENSG00000294798 ENST00000726050.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 13 publications found

Genes affected

ENSG00000294798 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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
ENSG00000294798	ENST00000726050.1	n.719G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47044 AN: 151840 Hom.: 8609 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.310 AC: 47072 AN: 151958 Hom.: 8612 Cov.: 31 AF XY: 0.314 AC XY: 23331 AN XY: 74250

African (AFR) AF: 0.447 AC: 18531 AN: 41424

American (AMR) AF: 0.292 AC: 4447 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 719 AN: 3468

East Asian (EAS) AF: 0.722 AC: 3738 AN: 5174

South Asian (SAS) AF: 0.424 AC: 2042 AN: 4814

European-Finnish (FIN) AF: 0.236 AC: 2490 AN: 10556

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14142 AN: 67968

Other (OTH) AF: 0.297 AC: 627 AN: 2114

Alfa AF: 0.243 Hom.: 2705

Bravo AF: 0.320

Asia WGS AF: 0.543 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.38
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4659444; hg19: chr1-26825116;