1-159753330-C-T

Variant names:

• chr1-159753330-C-T
• rs6677719
• ENST00000751880.1:n.325-10096G>A

Variant summary

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

The ENST00000751880.1(ENSG00000297934):​n.325-10096G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,186 control chromosomes in the GnomAD database, including 45,868 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 (45868 hom., cov: 32)
• Consequence: ENSG00000297934 ENST00000751880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.987
• Publications: 3 publications found

Genes affected

ENSG00000297934 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751880.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297934	ENST00000751880.1		n.325-10096G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116625 AN: 152068 Hom.: 45808 Cov.: 32

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.767 AC: 116742 AN: 152186 Hom.: 45868 Cov.: 32 AF XY: 0.766 AC XY: 57015 AN XY: 74404

African (AFR) AF: 0.942 AC: 39144 AN: 41546

American (AMR) AF: 0.804 AC: 12286 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3470

East Asian (EAS) AF: 0.839 AC: 4345 AN: 5176

South Asian (SAS) AF: 0.662 AC: 3198 AN: 4828

European-Finnish (FIN) AF: 0.698 AC: 7383 AN: 10580

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.668 AC: 45385 AN: 67984

Other (OTH) AF: 0.763 AC: 1612 AN: 2112

Alfa AF: 0.724 Hom.: 5025

Bravo AF: 0.786

Asia WGS AF: 0.754 AC: 2624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.9
DANN	Benign	0.59
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs6677719; hg19: chr1-159723120;