2-120355180-C-G

Variant names:

• chr2-120355180-C-G
• rs745723

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 0.153 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.152 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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0960

Gnomad4 OTH AF: 0.134

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs745723; hg19: chr2-121112756;