chr2-105446823-G-A

Variant names:

• chr2-105446823-G-A
• rs10496393

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0745 in 152,114 control chromosomes in the GnomAD database, including 749 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 0.075 (749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.0745 AC: 11319 AN: 151996 Hom.: 746 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0624

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0745 AC: 11338 AN: 152114 Hom.: 749 Cov.: 32 AF XY: 0.0793 AC XY: 5894 AN XY: 74352

African (AFR) AF: 0.109 AC: 4541 AN: 41524

American (AMR) AF: 0.0619 AC: 946 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0624 AC: 216 AN: 3464

East Asian (EAS) AF: 0.355 AC: 1824 AN: 5136

South Asian (SAS) AF: 0.0664 AC: 319 AN: 4806

European-Finnish (FIN) AF: 0.107 AC: 1135 AN: 10590

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2196 AN: 68002

Other (OTH) AF: 0.0678 AC: 143 AN: 2110

Alfa AF: 0.0461 Hom.: 1319

Bravo AF: 0.0753

Asia WGS AF: 0.185 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.36
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10496393; hg19: chr2-106063280;