1-159683149-C-T

Variant names:

• chr1-159683149-C-T
• rs2592887
• ENST00000751816.1:n.107+22460C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.107+22460C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,782 control chromosomes in the GnomAD database, including 14,516 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 0.43 (14516 hom., cov: 30)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 26 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.107+22460C>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.109+22460C>T		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.62+22460C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65854 AN: 151664 Hom.: 14494 Cov.: 30

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.434 AC: 65916 AN: 151782 Hom.: 14516 Cov.: 30 AF XY: 0.435 AC XY: 32244 AN XY: 74168

African (AFR) AF: 0.480 AC: 19847 AN: 41360

American (AMR) AF: 0.449 AC: 6848 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1403 AN: 3470

East Asian (EAS) AF: 0.581 AC: 2992 AN: 5146

South Asian (SAS) AF: 0.340 AC: 1635 AN: 4808

European-Finnish (FIN) AF: 0.398 AC: 4181 AN: 10514

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27435 AN: 67930

Other (OTH) AF: 0.424 AC: 893 AN: 2106

Alfa AF: 0.414 Hom.: 40066

Bravo AF: 0.440

Asia WGS AF: 0.464 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.42
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2592887; hg19: chr1-159652939;