1-1161720-C-T

Variant names:

• chr1-1161720-C-T
• rs1539634
• XR_007065350.1:n.2228C>T

Variant summary

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

The XR_007065350.1(LOC124903820):​n.2228C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,000 control chromosomes in the GnomAD database, including 58,456 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 0.87 (58456 hom., cov: 31)
• Consequence: LOC124903820 XR_007065350.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 3 publications found

Genes affected

LOC124903820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132567 AN: 151882 Hom.: 58415 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.873 AC: 132666 AN: 152000 Hom.: 58456 Cov.: 31 AF XY: 0.871 AC XY: 64758 AN XY: 74328

African (AFR) AF: 0.798 AC: 33072 AN: 41464

American (AMR) AF: 0.893 AC: 13648 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3125 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3036 AN: 5132

South Asian (SAS) AF: 0.878 AC: 4234 AN: 4822

European-Finnish (FIN) AF: 0.900 AC: 9535 AN: 10598

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63017 AN: 67918

Other (OTH) AF: 0.867 AC: 1831 AN: 2112

Alfa AF: 0.896 Hom.: 7142

Bravo AF: 0.866

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1539634; hg19: chr1-1097100;