rs1339048

Variant names:

• chr10-18941941-T-A
• rs1339048

Your query was ambiguous. Multiple possible variants found:

• chr10-18941941-T-A
• chr10-18941941-T-C
• chr10-18941941-T-G

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 0.446 in 151,934 control chromosomes in the GnomAD database, including 15,543 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 0.45 (15543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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: 0.446 AC: 67752 AN: 151814 Hom.: 15533 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.446 AC: 67814 AN: 151934 Hom.: 15543 Cov.: 32 AF XY: 0.448 AC XY: 33274 AN XY: 74234

African (AFR) AF: 0.556 AC: 23017 AN: 41432

American (AMR) AF: 0.389 AC: 5925 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1838 AN: 5176

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4822

European-Finnish (FIN) AF: 0.425 AC: 4483 AN: 10548

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27063 AN: 67932

Other (OTH) AF: 0.450 AC: 947 AN: 2106

Alfa AF: 0.308 Hom.: 810

Bravo AF: 0.440

Asia WGS AF: 0.487 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.79
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1339048; hg19: chr10-19230870;