rs10207814

Variant names:

• chr2-203595238-C-T
• rs10207814

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 0.0556 in 152,252 control chromosomes in the GnomAD database, including 350 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 0.056 (350 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.98
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0984 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: 0.0553 AC: 8420 AN: 152134 Hom.: 345 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0370

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0556 AC: 8459 AN: 152252 Hom.: 350 Cov.: 33 AF XY: 0.0541 AC XY: 4025 AN XY: 74458

African (AFR) AF: 0.101 AC: 4193 AN: 41530

American (AMR) AF: 0.0374 AC: 571 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3472

East Asian (EAS) AF: 0.103 AC: 536 AN: 5186

South Asian (SAS) AF: 0.0497 AC: 240 AN: 4830

European-Finnish (FIN) AF: 0.0120 AC: 127 AN: 10614

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0382 AC: 2597 AN: 68024

Other (OTH) AF: 0.0445 AC: 94 AN: 2114

Alfa AF: 0.0433 Hom.: 213

Bravo AF: 0.0596

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.18
PhyloP100		-5.0

Splicing

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

Other links and lift over

dbSNP: rs10207814; hg19: chr2-204459961;