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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376735	XR_001737778.2	n.476+358A>G		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;