rs10514769

Positions:

• chr2-30388682-G-C

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 0.15 in 152,116 control chromosomes in the GnomAD database, including 1,936 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 0.15 (1936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22833 AN: 151996 Hom.: 1936 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.150 AC: 22834 AN: 152116 Hom.: 1936 Cov.: 32 AF XY: 0.150 AC XY: 11172 AN XY: 74340

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.161

Alfa AF: 0.168 Hom.: 304

Bravo AF: 0.140

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514769; hg19: chr2-30611548;