2-122846942-T-G

Position:

• chr2-122846942-T-G

Variant summary

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

The ENST00000657880.1(ENSG00000286481):​n.837+23125T>G 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 0.825 in 152,002 control chromosomes in the GnomAD database, including 51,747 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 0.82 (51747 hom., cov: 31)
• Consequence: ENST00000657880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.875 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.837+23125T>G		intron_variant, non_coding_transcript_variant
	ENST00000687364.1	n.147+23125T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125250 AN: 151884 Hom.: 51696 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.825 AC: 125358 AN: 152002 Hom.: 51747 Cov.: 31 AF XY: 0.825 AC XY: 61279 AN XY: 74298

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.826

Alfa AF: 0.752 Hom.: 2232

Bravo AF: 0.825

Asia WGS AF: 0.878 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs296036; hg19: chr2-123604518;