2-187736531-C-T

Position:

• chr2-187736531-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 0.657 in 151,572 control chromosomes in the GnomAD database, including 35,679 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 0.66 (35679 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.187736531C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01090	ENST00000434418.2	n.497-23652G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99625 AN: 151454 Hom.: 35671 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.657 AC: 99653 AN: 151572 Hom.: 35679 Cov.: 32 AF XY: 0.661 AC XY: 48978 AN XY: 74070

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.680

Alfa AF: 0.719 Hom.: 10730

Bravo AF: 0.639

Asia WGS AF: 0.626 AC: 2149 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1520475; hg19: chr2-188601258;