2-133811726-T-G

Variant names:

• chr2-133811726-T-G
• rs7584077

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 0.863 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.802 AC: 32243 AN: 40192

American (AMR) AF: 0.884 AC: 13231 AN: 14962

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3138 AN: 3450

East Asian (EAS) AF: 0.963 AC: 4895 AN: 5082

South Asian (SAS) AF: 0.889 AC: 4198 AN: 4724

European-Finnish (FIN) AF: 0.866 AC: 8024 AN: 9270

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.882 AC: 59381 AN: 67334

Other (OTH) AF: 0.856 AC: 1788 AN: 2088

Alfa AF: 0.877 Hom.: 172297

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7584077; hg19: chr2-134569297;