1-159722783-T-C

Variant names:

• chr1-159722783-T-C
• rs2808634
• ENST00000751816.1:n.108-3744T>C

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-3744T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,086 control chromosomes in the GnomAD database, including 45,887 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 0.77 (45887 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 20 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 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.108-3744T>C		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-3744T>C		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-3744T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117664 AN: 151968 Hom.: 45835 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.774 AC: 117776 AN: 152086 Hom.: 45887 Cov.: 31 AF XY: 0.776 AC XY: 57715 AN XY: 74350

African (AFR) AF: 0.854 AC: 35442 AN: 41496

American (AMR) AF: 0.799 AC: 12205 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2879 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4252 AN: 5152

South Asian (SAS) AF: 0.668 AC: 3219 AN: 4820

European-Finnish (FIN) AF: 0.802 AC: 8485 AN: 10580

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48851 AN: 67976

Other (OTH) AF: 0.781 AC: 1644 AN: 2104

Alfa AF: 0.743 Hom.: 67461

Bravo AF: 0.779

Asia WGS AF: 0.741 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.44
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2808634; hg19: chr1-159692573;