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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656143.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227240	ENST00000656143.2		n.154-38871C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2039759;

hg19: chr1-193603469;