2-210745177-C-G

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 0.149 in 152,106 control chromosomes in the GnomAD database, including 2,145 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 (2145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 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: 0.149 AC: 22702 AN: 151988 Hom.: 2141 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.149 AC: 22703 AN: 152106 Hom.: 2145 Cov.: 32 AF XY: 0.155 AC XY: 11553 AN XY: 74348

Gnomad4 AFR AF: 0.0348

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0737 Hom.: 132

Bravo AF: 0.138

Asia WGS AF: 0.161 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.6
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490325; hg19: chr2-211609901;