1-159665231-C-T

Variant names:

• chr1-159665231-C-T
• rs2794500
• ENST00000751816.1:n.107+4542C>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+4542C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,944 control chromosomes in the GnomAD database, including 16,149 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 0.44 (16149 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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
ENSG00000297913	ENST00000751816.1	n.107+4542C>T		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.109+4542C>T		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.62+4542C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66111 AN: 151826 Hom.: 16127 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.436 AC: 66185 AN: 151944 Hom.: 16149 Cov.: 31 AF XY: 0.430 AC XY: 31962 AN XY: 74244

African (AFR) AF: 0.671 AC: 27818 AN: 41438

American (AMR) AF: 0.309 AC: 4713 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1417 AN: 3470

East Asian (EAS) AF: 0.158 AC: 816 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1443 AN: 4814

European-Finnish (FIN) AF: 0.388 AC: 4080 AN: 10522

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24657 AN: 67952

Other (OTH) AF: 0.416 AC: 876 AN: 2106

Alfa AF: 0.379 Hom.: 9009

Bravo AF: 0.439

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.23
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2794500; hg19: chr1-159635021;