1-1159358-A-G

Variant names:

• chr1-1159358-A-G
• rs4970362
• XR_007065350.1:n.996+674A>G

Variant summary

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

The XR_007065350.1(LOC124903820):​n.996+674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,008 control chromosomes in the GnomAD database, including 28,796 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 0.61 (28796 hom., cov: 33)
• Consequence: LOC124903820 XR_007065350.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 7 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.72 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: 0.610 AC: 92583 AN: 151890 Hom.: 28762 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.610 AC: 92662 AN: 152008 Hom.: 28796 Cov.: 33 AF XY: 0.610 AC XY: 45319 AN XY: 74280

African (AFR) AF: 0.517 AC: 21445 AN: 41470

American (AMR) AF: 0.731 AC: 11183 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2419 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2764 AN: 5148

South Asian (SAS) AF: 0.672 AC: 3248 AN: 4832

European-Finnish (FIN) AF: 0.576 AC: 6080 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43334 AN: 67934

Other (OTH) AF: 0.639 AC: 1349 AN: 2112

Alfa AF: 0.633 Hom.: 21922

Bravo AF: 0.616

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs4970362; hg19: chr1-1094738; COSMIC: COSV52468699;