rs13020676

Positions:

• chr2-22003535-G-A
• chr2-22003535-G-T

Variant summary

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

The ENST00000450551.1(ENSG00000228999):​n.201-31699C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.23 (3170 hom., cov: 20)
• Consequence: ENST00000450551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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
	ENST00000450551.1	n.201-31699C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.231 AC: 27081 AN: 117050 Hom.: 3168 Cov.: 20

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.231 AC: 27082 AN: 117080 Hom.: 3170 Cov.: 20 AF XY: 0.232 AC XY: 12681 AN XY: 54758

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.0115

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.244

Alfa AF: 0.183 Hom.: 924

Bravo AF: 0.185

Asia WGS AF: 0.0780 AC: 272 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13020676; hg19: chr2-22226407;