2-207490606-A-G

Position:

• chr2-207490606-A-G

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+27014T>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 0.367 in 146,340 control chromosomes in the GnomAD database, including 13,116 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 0.37 (13116 hom., cov: 28)
• Consequence: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 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+27014T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.256+27014T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 53600 AN: 146218 Hom.: 13098 Cov.: 28

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.367 AC: 53668 AN: 146340 Hom.: 13116 Cov.: 28 AF XY: 0.371 AC XY: 26456 AN XY: 71398

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.354

Alfa AF: 0.363 Hom.: 1486

Asia WGS AF: 0.372 AC: 1293 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72954151; hg19: chr2-208355330;