1-159709026-C-T

Variant names:

• chr1-159709026-C-T
• rs2794520
• ENST00000751816.1:n.108-17501C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-17501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,928 control chromosomes in the GnomAD database, including 8,107 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 0.32 (8107 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 128 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 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.108-17501C>T		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-17501C>T		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-17501C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48021 AN: 151810 Hom.: 8100 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.316 AC: 48046 AN: 151928 Hom.: 8107 Cov.: 31 AF XY: 0.321 AC XY: 23798 AN XY: 74246

African (AFR) AF: 0.214 AC: 8874 AN: 41434

American (AMR) AF: 0.375 AC: 5720 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3466

East Asian (EAS) AF: 0.582 AC: 3002 AN: 5156

South Asian (SAS) AF: 0.306 AC: 1470 AN: 4802

European-Finnish (FIN) AF: 0.376 AC: 3955 AN: 10530

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22777 AN: 67962

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.332 Hom.: 40786

Bravo AF: 0.312

Asia WGS AF: 0.438 AC: 1522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.72
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2794520; hg19: chr1-159678816;