rs1360550

Variant names:

• chr10-30198831-G-A
• rs1360550
• XR_930791.2:n.1448+559G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-30198831-G-A
• chr10-30198831-G-C
• chr10-30198831-G-T

Variant summary

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

The XR_930791.2(LOC105376477):​n.1448+559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,020 control chromosomes in the GnomAD database, including 22,971 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 0.51 (22971 hom., cov: 31)
• Consequence: LOC105376477 XR_930791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 10 publications found

Genes affected

LOC105376477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 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: 0.507 AC: 76957 AN: 151902 Hom.: 22965 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.506 AC: 76960 AN: 152020 Hom.: 22971 Cov.: 31 AF XY: 0.510 AC XY: 37880 AN XY: 74310

African (AFR) AF: 0.194 AC: 8056 AN: 41476

American (AMR) AF: 0.557 AC: 8508 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2136 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1241 AN: 5172

South Asian (SAS) AF: 0.516 AC: 2488 AN: 4820

European-Finnish (FIN) AF: 0.742 AC: 7831 AN: 10558

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.659 AC: 44734 AN: 67926

Other (OTH) AF: 0.523 AC: 1103 AN: 2108

Alfa AF: 0.411 Hom.: 1862

Bravo AF: 0.476

Asia WGS AF: 0.370 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.76
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs1360550; hg19: chr10-30487760;