rs10036001

Variant names:

• chr5-5850299-G-A
• rs10036001

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 0.219 in 152,024 control chromosomes in the GnomAD database, including 3,740 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 (3740 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.219 AC: 33272 AN: 151906 Hom.: 3739 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.219 AC: 33282 AN: 152024 Hom.: 3740 Cov.: 32 AF XY: 0.222 AC XY: 16526 AN XY: 74322

African (AFR) AF: 0.203 AC: 8417 AN: 41464

American (AMR) AF: 0.178 AC: 2715 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1388 AN: 5158

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4814

European-Finnish (FIN) AF: 0.264 AC: 2787 AN: 10552

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15734 AN: 67960

Other (OTH) AF: 0.171 AC: 362 AN: 2112

Alfa AF: 0.221 Hom.: 953

Bravo AF: 0.210

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10036001; hg19: chr5-5850412;