2-207493114-T-C

Position:

• chr2-207493114-T-C

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+24506A>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 0.873 in 146,784 control chromosomes in the GnomAD database, including 57,612 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 0.87 (57612 hom., cov: 29)
• Consequence: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
	ENST00000412387.5	n.260+24506A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.256+24506A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.873 AC: 128023 AN: 146664 Hom.: 57565 Cov.: 29

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.894

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.873 AC: 128129 AN: 146784 Hom.: 57612 Cov.: 29 AF XY: 0.877 AC XY: 62761 AN XY: 71552

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.951

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.900

Alfa AF: 0.874 Hom.: 38185

Asia WGS AF: 0.944 AC: 3275 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959668; hg19: chr2-208357838;