1-159714875-G-T

Variant names:

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

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-11652G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,990 control chromosomes in the GnomAD database, including 1,834 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 0.13 (1834 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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.108-11652G>T		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-11652G>T		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-11652G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18994 AN: 151872 Hom.: 1826 Cov.: 30

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.125 AC: 19027 AN: 151990 Hom.: 1834 Cov.: 30 AF XY: 0.124 AC XY: 9205 AN XY: 74274

African (AFR) AF: 0.265 AC: 10993 AN: 41424

American (AMR) AF: 0.0746 AC: 1141 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3472

East Asian (EAS) AF: 0.152 AC: 783 AN: 5150

South Asian (SAS) AF: 0.102 AC: 489 AN: 4814

European-Finnish (FIN) AF: 0.0652 AC: 688 AN: 10556

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4173 AN: 67972

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.00139 Hom.: 12835

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.026
DANN	Benign	0.55
PhyloP100		-1.7
PromoterAI		-0.0085	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;