rs3124203

Variant names:

• chr10-30510787-C-G
• rs3124203

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 0.212 in 152,058 control chromosomes in the GnomAD database, including 3,945 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 0.21 (3945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.212 AC: 32206 AN: 151940 Hom.: 3946 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.212 AC: 32203 AN: 152058 Hom.: 3945 Cov.: 32 AF XY: 0.211 AC XY: 15676 AN XY: 74312

African (AFR) AF: 0.0961 AC: 3988 AN: 41512

American (AMR) AF: 0.254 AC: 3875 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3468

East Asian (EAS) AF: 0.0794 AC: 410 AN: 5166

South Asian (SAS) AF: 0.247 AC: 1189 AN: 4818

European-Finnish (FIN) AF: 0.240 AC: 2534 AN: 10546

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18532 AN: 67974

Other (OTH) AF: 0.236 AC: 498 AN: 2114

Alfa AF: 0.241 Hom.: 582

Bravo AF: 0.204

Asia WGS AF: 0.143 AC: 498 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.48
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs3124203; hg19: chr10-30799716;