chr2-133811726-T-G

Position:

• chr2-133811726-T-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 0.863 in 148,304 control chromosomes in the GnomAD database, including 55,296 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 0.86 (55296 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.863 AC: 127851 AN: 148194 Hom.: 55260 Cov.: 23

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.861

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.863 AC: 127939 AN: 148304 Hom.: 55296 Cov.: 23 AF XY: 0.865 AC XY: 62544 AN XY: 72272

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.856

Alfa AF: 0.882 Hom.: 75285

Bravo AF: 0.862

Asia WGS AF: 0.914 AC: 3175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.38
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7584077; hg19: chr2-134569297;