chr2-101975535-T-C

Position:

• chr2-101975535-T-C

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 0.724 in 151,906 control chromosomes in the GnomAD database, including 40,326 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 0.72 (40326 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.85

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101975535T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01127	ENST00000627215.1	n.252-8157T>C		intron_variant		2
LINC01127	ENST00000627273.3	n.256-8157T>C		intron_variant		4
LINC01127	ENST00000702456.1	n.242-8157T>C		intron_variant
LINC01127	ENST00000702641.1	n.246-8157T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109815 AN: 151788 Hom.: 40282 Cov.: 29

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.724 AC: 109909 AN: 151906 Hom.: 40326 Cov.: 29 AF XY: 0.730 AC XY: 54218 AN XY: 74222

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.706

Alfa AF: 0.708 Hom.: 4747

Bravo AF: 0.723

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.022
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12712122; hg19: chr2-102591997;