rs10495728

Variant names:

• chr2-22677249-G-A
• rs10495728

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;