rs10011000

Variant names:

• chr4-71868845-C-G
• rs10011000

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 0.224 in 151,964 control chromosomes in the GnomAD database, including 4,027 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 0.22 (4027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.309 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: 0.224 AC: 34046 AN: 151846 Hom.: 4033 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.224 AC: 34045 AN: 151964 Hom.: 4027 Cov.: 32 AF XY: 0.224 AC XY: 16602 AN XY: 74232

African (AFR) AF: 0.158 AC: 6550 AN: 41472

American (AMR) AF: 0.181 AC: 2771 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3464

East Asian (EAS) AF: 0.322 AC: 1665 AN: 5168

South Asian (SAS) AF: 0.279 AC: 1344 AN: 4812

European-Finnish (FIN) AF: 0.243 AC: 2562 AN: 10526

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17643 AN: 67940

Other (OTH) AF: 0.226 AC: 476 AN: 2110

Alfa AF: 0.245 Hom.: 574

Bravo AF: 0.215

Asia WGS AF: 0.263 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.57
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10011000; hg19: chr4-72734562;