1-159710123-G-T

Variant names:

• chr1-159710123-G-T
• rs3093075
• ENST00000751816.1:n.108-16404G>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-16404G>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 152,114 control chromosomes in the GnomAD database, including 1,829 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 (1829 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 25 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-16404G>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-16404G>T		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-16404G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19053 AN: 151998 Hom.: 1821 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.125 AC: 19084 AN: 152114 Hom.: 1829 Cov.: 32 AF XY: 0.124 AC XY: 9251 AN XY: 74374

African (AFR) AF: 0.265 AC: 10993 AN: 41444

American (AMR) AF: 0.0747 AC: 1142 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.155 AC: 799 AN: 5170

South Asian (SAS) AF: 0.106 AC: 509 AN: 4818

European-Finnish (FIN) AF: 0.0663 AC: 703 AN: 10596

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

European-Non Finnish (NFE) AF: 0.0614 AC: 4175 AN: 68006

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.162 Hom.: 726

Bravo AF: 0.132

Asia WGS AF: 0.110 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.80
DANN	Benign	0.54
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs3093075; hg19: chr1-159679913;