rs1358520

Positions:

• chr2-180575354-G-A
• chr2-180575354-G-T

Variant summary

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

The ENST00000429816.1(ENSG00000225258):​n.443-3523C>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 0.229 in 151,300 control chromosomes in the GnomAD database, including 4,385 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 0.23 (4385 hom., cov: 32)
• Consequence: ENST00000429816.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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
	ENST00000429816.1	n.443-3523C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34536 AN: 151182 Hom.: 4368 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.229 AC: 34592 AN: 151300 Hom.: 4385 Cov.: 32 AF XY: 0.234 AC XY: 17301 AN XY: 73918

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.213

Alfa AF: 0.221 Hom.: 6362

Bravo AF: 0.237

Asia WGS AF: 0.395 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358520; hg19: chr2-181440081;