chr2-206868387-C-T

Variant names:

• chr2-206868387-C-T
• rs4673364
• ENST00000438070.3:n.1338C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438070.3(ENSG00000229321):​n.1338C>T variant causes a non coding transcript exon 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: ENSG00000229321 ENST00000438070.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 5 publications found

Genes affected

ENSG00000229321 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229321	ENST00000438070.3	n.1338C>T		non_coding_transcript_exon_variant	Exon 5 of 7	3
ENSG00000229321	ENST00000658889.1	n.2974-10996C>T		intron_variant	Intron 1 of 4
ENSG00000229321	ENST00000659096.2	n.663-836C>T		intron_variant	Intron 4 of 6
ENSG00000229321	ENST00000765098.1	n.448+394C>T		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.0725 AC: 3010 AN: 41496

American (AMR) AF: 0.0820 AC: 1253 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1063 AN: 5164

South Asian (SAS) AF: 0.168 AC: 809 AN: 4818

European-Finnish (FIN) AF: 0.131 AC: 1382 AN: 10574

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8216 AN: 67994

Other (OTH) AF: 0.105 AC: 222 AN: 2112

Alfa AF: 0.117 Hom.: 4592

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
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4673364; hg19: chr2-207733111;