rs10495864

chr2-36061605-T-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 0.0281 in 151,918 control chromosomes in the GnomAD database, including 236 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 0.028 (236 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 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: 0.0280 AC: 4253 AN: 151798 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.00994

Gnomad FIN AF: 0.000941

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00332

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0281 AC: 4269 AN: 151918 Hom.: 236 Cov.: 32 AF XY: 0.0298 AC XY: 2210 AN XY: 74244

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.0290

Gnomad4 SAS AF: 0.00995

Gnomad4 FIN AF: 0.000941

Gnomad4 NFE AF: 0.00332

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0159 Hom.: 14

Bravo AF: 0.0402

Asia WGS AF: 0.0270 AC: 95 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.7
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495864; hg19: chr2-36288748;