chr2-120437605-A-G

Position:

• chr2-120437605-A-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 0.16 in 152,070 control chromosomes in the GnomAD database, including 2,777 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 0.16 (2777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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: 0.159 AC: 24209 AN: 151952 Hom.: 2767 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0880

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.160 AC: 24257 AN: 152070 Hom.: 2777 Cov.: 32 AF XY: 0.159 AC XY: 11801 AN XY: 74352

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.0880

Gnomad4 OTH AF: 0.150

Alfa AF: 0.106 Hom.: 1631

Bravo AF: 0.167

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7581710; hg19: chr2-121195181;