rs10495728

chr2-22677249-G-A

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 0.244 in 152,098 control chromosomes in the GnomAD database, including 5,315 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 0.24 (5315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 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: 0.245 AC: 37166 AN: 151980 Hom.: 5305 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.244 AC: 37184 AN: 152098 Hom.: 5315 Cov.: 32 AF XY: 0.251 AC XY: 18622 AN XY: 74338

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.276

Alfa AF: 0.273 Hom.: 11600

Bravo AF: 0.238

Asia WGS AF: 0.342 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.34
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495728; hg19: chr2-22900121;