2-133941727-C-T

Position:

• chr2-133941727-C-T

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 0.693 in 151,966 control chromosomes in the GnomAD database, including 36,660 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 0.69 (36660 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133941727C>T		intergenic_region
LOC105373627	XR_001739714.2	n.1936+11200G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105180 AN: 151848 Hom.: 36639 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.693 AC: 105258 AN: 151966 Hom.: 36660 Cov.: 31 AF XY: 0.687 AC XY: 51006 AN XY: 74280

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.682

Alfa AF: 0.653 Hom.: 3663

Bravo AF: 0.691

Asia WGS AF: 0.584 AC: 2029 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13388210; hg19: chr2-134699298;