2-70836812-C-T

Variant names:

• chr2-70836812-C-T
• rs4852708

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 0.151 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
• Publications: 9 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 (AMR) allele frequency at 95% confidence interval = 0.182 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: 0.151 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

African (AFR) AF: 0.161 AC: 6686 AN: 41480

American (AMR) AF: 0.188 AC: 2877 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.151 AC: 782 AN: 5180

South Asian (SAS) AF: 0.163 AC: 787 AN: 4814

European-Finnish (FIN) AF: 0.182 AC: 1921 AN: 10578

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8832 AN: 68002

Other (OTH) AF: 0.141 AC: 297 AN: 2108

Alfa AF: 0.135 Hom.: 4081

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4852708; hg19: chr2-71063942;