rs10900029

Variant names:

• chr10-44366772-G-A
• rs10900029

Your query was ambiguous. Multiple possible variants found:

• chr10-44366772-G-A
• chr10-44366772-G-C
• chr10-44366772-G-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 0.193 in 152,078 control chromosomes in the GnomAD database, including 3,222 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 0.19 (3222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 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: 0.193 AC: 29253 AN: 151960 Hom.: 3212 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.193 AC: 29277 AN: 152078 Hom.: 3222 Cov.: 32 AF XY: 0.195 AC XY: 14505 AN XY: 74346

African (AFR) AF: 0.108 AC: 4478 AN: 41498

American (AMR) AF: 0.199 AC: 3036 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3468

East Asian (EAS) AF: 0.430 AC: 2214 AN: 5150

South Asian (SAS) AF: 0.288 AC: 1384 AN: 4810

European-Finnish (FIN) AF: 0.204 AC: 2155 AN: 10582

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14368 AN: 67970

Other (OTH) AF: 0.228 AC: 481 AN: 2114

Alfa AF: 0.204 Hom.: 10673

Bravo AF: 0.187

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.63
DANN	Benign	0.33
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10900029; hg19: chr10-44862220;