chr1-1161955-T-G

Variant names:

• chr1-1161955-T-G
• rs9442385
• XR_007065350.1:n.*15T>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.*15T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,170 control chromosomes in the GnomAD database, including 59,196 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 0.88 (59196 hom., cov: 33)
• Consequence: LOC124903820 XR_007065350.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.32
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133546 AN: 152052 Hom.: 59152 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.878 AC: 133648 AN: 152170 Hom.: 59196 Cov.: 33 AF XY: 0.876 AC XY: 65193 AN XY: 74388

African (AFR) AF: 0.816 AC: 33891 AN: 41516

American (AMR) AF: 0.895 AC: 13702 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3127 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3050 AN: 5142

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

European-Finnish (FIN) AF: 0.900 AC: 9531 AN: 10594

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

European-Non Finnish (NFE) AF: 0.928 AC: 63105 AN: 68000

Other (OTH) AF: 0.870 AC: 1840 AN: 2114

Alfa AF: 0.909 Hom.: 204183

Bravo AF: 0.872

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.010
DANN	Benign	0.20
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs9442385; hg19: chr1-1097335;