2-120355180-C-G

Variant names:

• chr2-120355180-C-G
• rs745723

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 0.153 in 152,168 control chromosomes in the GnomAD database, including 2,195 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 (2195 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23176 AN: 152050 Hom.: 2182 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.153 AC: 23223 AN: 152168 Hom.: 2195 Cov.: 33 AF XY: 0.155 AC XY: 11510 AN XY: 74398

African (AFR) AF: 0.225 AC: 9323 AN: 41494

American (AMR) AF: 0.206 AC: 3148 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3472

East Asian (EAS) AF: 0.350 AC: 1809 AN: 5166

South Asian (SAS) AF: 0.107 AC: 515 AN: 4814

European-Finnish (FIN) AF: 0.100 AC: 1062 AN: 10598

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0960 AC: 6526 AN: 68014

Other (OTH) AF: 0.134 AC: 282 AN: 2110

Alfa AF: 0.0525 Hom.: 48

Bravo AF: 0.168

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.75
DANN	Benign	0.40
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs745723; hg19: chr2-121112756;