chr2-206868387-C-T

Position:

• chr2-206868387-C-T

Variant summary

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

The ENST00000658889.1(ENSG00000229321):​n.2974-10996C>T 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 0.11 in 152,118 control chromosomes in the GnomAD database, including 1,015 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 0.11 (1015 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000658889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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
	ENST00000658889.1	n.2974-10996C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16727 AN: 152000 Hom.: 1012 Cov.: 32

Gnomad AFR AF: 0.0728

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.0820

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.110 AC: 16729 AN: 152118 Hom.: 1015 Cov.: 32 AF XY: 0.112 AC XY: 8299 AN XY: 74358

Gnomad4 AFR AF: 0.0725

Gnomad4 AMR AF: 0.0820

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.105

Alfa AF: 0.117 Hom.: 2270

Bravo AF: 0.104

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.013
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4673364; hg19: chr2-207733111;