rs1358030

Variant names:

• chr10-106363841-G-A
• rs1358030

Your query was ambiguous. Multiple possible variants found:

• chr10-106363841-G-A
• chr10-106363841-G-C

Variant summary

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

The variant allele was found at a frequency of 0.571 in 152,118 control chromosomes in the GnomAD database, including 25,421 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 0.57 (25421 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86793 AN: 152000 Hom.: 25409 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.571 AC: 86836 AN: 152118 Hom.: 25421 Cov.: 33 AF XY: 0.567 AC XY: 42155 AN XY: 74360

African (AFR) AF: 0.498 AC: 20646 AN: 41496

American (AMR) AF: 0.506 AC: 7735 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1840 AN: 5182

South Asian (SAS) AF: 0.513 AC: 2475 AN: 4828

European-Finnish (FIN) AF: 0.609 AC: 6429 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44100 AN: 67980

Other (OTH) AF: 0.562 AC: 1186 AN: 2112

Alfa AF: 0.617 Hom.: 19459

Bravo AF: 0.557

Asia WGS AF: 0.392 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.40
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1358030; hg19: chr10-108123599;