1-1161955-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903820	XR_007065350.1	n.*15T>G		downstream_gene_variant
LOC124903820	XR_007065351.1	n.*15T>G		downstream_gene_variant

Ensembl

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

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 v4.3

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;