chr2-70836812-C-T

Position:

• chr2-70836812-C-T

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 0.151 in 152,122 control chromosomes in the GnomAD database, including 1,820 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 (1820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22927 AN: 152004 Hom.: 1824 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.151 AC: 22931 AN: 152122 Hom.: 1820 Cov.: 32 AF XY: 0.153 AC XY: 11368 AN XY: 74346

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.141

Alfa AF: 0.128 Hom.: 1515

Bravo AF: 0.154

Asia WGS AF: 0.189 AC: 653 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	0.086
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4852708; hg19: chr2-71063942;