rs10883437

Variant names:

• chr10-100035604-T-A
• rs10883437

Your query was ambiguous. Multiple possible variants found:

• chr10-100035604-T-A
• chr10-100035604-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 0.423 in 152,034 control chromosomes in the GnomAD database, including 14,731 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 0.42 (14731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 23 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 (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.423 AC: 64267 AN: 151916 Hom.: 14696 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.423 AC: 64364 AN: 152034 Hom.: 14731 Cov.: 32 AF XY: 0.413 AC XY: 30712 AN XY: 74306

African (AFR) AF: 0.582 AC: 24140 AN: 41470

American (AMR) AF: 0.431 AC: 6571 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3466

East Asian (EAS) AF: 0.188 AC: 973 AN: 5178

South Asian (SAS) AF: 0.198 AC: 955 AN: 4820

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10574

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26180 AN: 67966

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.402 Hom.: 1596

Bravo AF: 0.447

Asia WGS AF: 0.211 AC: 736 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	0.31
DANN	Benign	0.087
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10883437; hg19: chr10-101795361;