1-159685936-G-T

Variant names:

• chr1-159685936-G-T
• rs2592902
• ENST00000751816.1:n.107+25247G>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+25247G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,030 control chromosomes in the GnomAD database, including 10,215 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 0.36 (10215 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 9 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=-0.64).
• 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+25247G>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.109+25247G>T		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.62+25247G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54324 AN: 151912 Hom.: 10209 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.357 AC: 54350 AN: 152030 Hom.: 10215 Cov.: 32 AF XY: 0.360 AC XY: 26732 AN XY: 74312

African (AFR) AF: 0.249 AC: 10324 AN: 41466

American (AMR) AF: 0.411 AC: 6281 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3008 AN: 5176

South Asian (SAS) AF: 0.339 AC: 1636 AN: 4822

European-Finnish (FIN) AF: 0.390 AC: 4103 AN: 10522

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26384 AN: 67968

Other (OTH) AF: 0.369 AC: 777 AN: 2108

Alfa AF: 0.215 Hom.: 1269

Bravo AF: 0.354

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.8
DANN	Benign	0.93
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2592902; hg19: chr1-159655726;