2-207491066-T-G

Position:

• chr2-207491066-T-G

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+26554A>C 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 0.388 in 146,962 control chromosomes in the GnomAD database, including 14,599 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 0.39 (14599 hom., cov: 29)
• Consequence: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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+26554A>C		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.256+26554A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.388 AC: 57002 AN: 146844 Hom.: 14575 Cov.: 29

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.388 AC: 57078 AN: 146962 Hom.: 14599 Cov.: 29 AF XY: 0.392 AC XY: 28134 AN XY: 71764

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.367

Alfa AF: 0.325 Hom.: 3515

Asia WGS AF: 0.374 AC: 1301 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs918843; hg19: chr2-208355790;