rs1159275

Variant names:

• chr1-195680112-G-T
• rs1159275
• XR_922391.1:n.241+10493C>A

Variant summary

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

The XR_922391.1(LOC105371671):​n.241+10493C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,998 control chromosomes in the GnomAD database, including 39,028 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 0.70 (39028 hom., cov: 32)
• Consequence: LOC105371671 XR_922391.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66
• Publications: 3 publications found

Genes affected

LOC105371671 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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: 0.705 AC: 107062 AN: 151880 Hom.: 39013 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.705 AC: 107125 AN: 151998 Hom.: 39028 Cov.: 32 AF XY: 0.699 AC XY: 51947 AN XY: 74288

African (AFR) AF: 0.553 AC: 22895 AN: 41430

American (AMR) AF: 0.665 AC: 10148 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2344 AN: 5146

South Asian (SAS) AF: 0.708 AC: 3413 AN: 4824

European-Finnish (FIN) AF: 0.769 AC: 8129 AN: 10572

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55579 AN: 67998

Other (OTH) AF: 0.687 AC: 1448 AN: 2108

Alfa AF: 0.741 Hom.: 7443

Bravo AF: 0.683

Asia WGS AF: 0.571 AC: 1982 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.44
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs1159275; hg19: chr1-195649242;