XR_001737778.2:n.476+358A>G

Variant names:

• chr1-10916638-T-C
• rs1280975
• XR_001737778.2:n.476+358A>G

Variant summary

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

The XR_001737778.2(LOC105376735):​n.476+358A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,232 control chromosomes in the GnomAD database, including 58,662 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 (58662 hom., cov: 32)
• Consequence: LOC105376735 XR_001737778.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 3 publications found

Genes affected

LOC105376735 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.876 AC: 133260 AN: 152114 Hom.: 58641 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.876 AC: 133333 AN: 152232 Hom.: 58662 Cov.: 32 AF XY: 0.880 AC XY: 65505 AN XY: 74448

African (AFR) AF: 0.777 AC: 32267 AN: 41504

American (AMR) AF: 0.921 AC: 14093 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3314 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4984 AN: 5180

South Asian (SAS) AF: 0.922 AC: 4447 AN: 4824

European-Finnish (FIN) AF: 0.946 AC: 10049 AN: 10618

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61091 AN: 68018

Other (OTH) AF: 0.902 AC: 1904 AN: 2112

Alfa AF: 0.895 Hom.: 80107

Bravo AF: 0.869

Asia WGS AF: 0.936 AC: 3256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.43
DANN	Benign	0.79
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1280975; hg19: chr1-10976695;