rs10207814

chr2-203595238-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0233

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.0120

Gnomad4 NFE AF: 0.0382

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0412 Hom.: 138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10207814; hg19: chr2-204459961;