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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903820	XR_007065350.1	n.2228C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124903820	XR_007065351.1	n.1510C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;