rs2382748

Variant names:

• chr10-47130383-A-C
• rs2382748

Your query was ambiguous. Multiple possible variants found:

• chr10-47130383-A-C
• chr10-47130383-A-T

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 0.0792 in 152,064 control chromosomes in the GnomAD database, including 1,086 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 0.079 (1086 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.0791 AC: 12026 AN: 151946 Hom.: 1083 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00548

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0221

Gnomad OTH AF: 0.0795

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

GnomAD4 genome AF: 0.0792 AC: 12046 AN: 152064 Hom.: 1086 Cov.: 33 AF XY: 0.0763 AC XY: 5674 AN XY: 74368

African (AFR) AF: 0.219 AC: 9065 AN: 41414

American (AMR) AF: 0.0528 AC: 807 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 344 AN: 3466

East Asian (EAS) AF: 0.000770 AC: 4 AN: 5192

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4822

European-Finnish (FIN) AF: 0.00548 AC: 58 AN: 10580

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0221 AC: 1505 AN: 67996

Other (OTH) AF: 0.0787 AC: 166 AN: 2110

Alfa AF: 0.0246 Hom.: 31

Bravo AF: 0.0904

Asia WGS AF: 0.0200 AC: 68 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.68
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs2382748; hg19: chr10-48608979;