rs2039759

Variant names:

• chr1-193634339-C-T
• rs2039759
• ENST00000656143.2:n.154-38871C>T

Variant summary

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

The ENST00000656143.2(ENSG00000227240):​n.154-38871C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,644 control chromosomes in the GnomAD database, including 18,193 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 0.47 (18193 hom., cov: 32)
• Consequence: ENSG00000227240 ENST00000656143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 4 publications found

Genes affected

ENSG00000227240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5234+160963C>T		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.2	n.154-38871C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70778 AN: 151526 Hom.: 18197 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.467 AC: 70796 AN: 151644 Hom.: 18193 Cov.: 32 AF XY: 0.469 AC XY: 34773 AN XY: 74102

African (AFR) AF: 0.268 AC: 11087 AN: 41376

American (AMR) AF: 0.581 AC: 8839 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2181 AN: 3458

East Asian (EAS) AF: 0.813 AC: 4189 AN: 5152

South Asian (SAS) AF: 0.603 AC: 2910 AN: 4822

European-Finnish (FIN) AF: 0.408 AC: 4305 AN: 10556

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35579 AN: 67780

Other (OTH) AF: 0.515 AC: 1077 AN: 2092

Alfa AF: 0.513 Hom.: 10534

Bravo AF: 0.477

Asia WGS AF: 0.647 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.5
DANN	Benign	0.65
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2039759; hg19: chr1-193603469;