rs10213084

Variant names:

• chr4-146578186-G-T
• rs10213084

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 0.121 in 152,088 control chromosomes in the GnomAD database, including 1,194 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 0.12 (1194 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 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: 0.121 AC: 18346 AN: 151970 Hom.: 1192 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.121 AC: 18360 AN: 152088 Hom.: 1194 Cov.: 32 AF XY: 0.117 AC XY: 8664 AN XY: 74340

African (AFR) AF: 0.149 AC: 6171 AN: 41488

American (AMR) AF: 0.0886 AC: 1354 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3470

East Asian (EAS) AF: 0.0297 AC: 154 AN: 5180

South Asian (SAS) AF: 0.104 AC: 500 AN: 4814

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10584

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8182 AN: 67960

Other (OTH) AF: 0.120 AC: 254 AN: 2112

Alfa AF: 0.122 Hom.: 1691

Bravo AF: 0.121

Asia WGS AF: 0.0860 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10213084; hg19: chr4-147499338;