1-159714875-G-A

Variant names:

• chr1-159714875-G-A
• rs3091244
• ENST00000751816.1:n.108-11652G>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-11652G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,984 control chromosomes in the GnomAD database, including 7,034 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 0.30 (7034 hom., cov: 30)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 163 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-11652G>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-11652G>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-11652G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45553 AN: 151866 Hom.: 7036 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.300 AC: 45581 AN: 151984 Hom.: 7034 Cov.: 30 AF XY: 0.299 AC XY: 22217 AN XY: 74276

African (AFR) AF: 0.291 AC: 12046 AN: 41434

American (AMR) AF: 0.319 AC: 4873 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3470

East Asian (EAS) AF: 0.0616 AC: 317 AN: 5150

South Asian (SAS) AF: 0.246 AC: 1183 AN: 4818

European-Finnish (FIN) AF: 0.355 AC: 3743 AN: 10556

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21353 AN: 67960

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.380 Hom.: 12835

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.053
DANN	Benign	0.67
PhyloP100		-1.7
PromoterAI		-0.0094	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3091244; hg19: chr1-159684665;