chr10-30198831-G-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376477	XR_930791.2	n.1448+559G>A		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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;