2-122732606-C-T

Position:

• chr2-122732606-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657880.1(ENSG00000286481):​n.774-91148C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,008 control chromosomes in the GnomAD database, including 1,671 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 0.14 (1671 hom., cov: 31)
• Consequence: ENST00000657880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 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
	ENST00000657880.1	n.774-91148C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21337 AN: 151890 Hom.: 1671 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.140 AC: 21355 AN: 152008 Hom.: 1671 Cov.: 31 AF XY: 0.145 AC XY: 10760 AN XY: 74270

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0926

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0635 Hom.: 64

Bravo AF: 0.146

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13000913; hg19: chr2-123490182;