2-207498338-C-T

Position:

• chr2-207498338-C-T

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+19282G>A 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 0.414 in 152,030 control chromosomes in the GnomAD database, including 13,715 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 0.41 (13715 hom., cov: 32)
• Consequence: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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+19282G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.256+19282G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62974 AN: 151910 Hom.: 13722 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.414 AC: 62975 AN: 152030 Hom.: 13715 Cov.: 32 AF XY: 0.418 AC XY: 31047 AN XY: 74298

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.450

Alfa AF: 0.434 Hom.: 29131

Bravo AF: 0.402

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2042484; hg19: chr2-208363062;