rs1820450

Variant names:

• chr15-34601063-C-G
• rs1820450
• ENST00000720812.1:n.118+12414C>G

Your query was ambiguous. Multiple possible variants found:

• chr15-34601063-C-G
• chr15-34601063-C-T

Variant summary

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

The ENST00000720812.1(ENSG00000287973):​n.118+12414C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,972 control chromosomes in the GnomAD database, including 17,327 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 0.46 (17327 hom., cov: 31)
• Consequence: ENSG00000287973 ENST00000720812.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 3 publications found

Genes affected

ENSG00000287973 (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 (AMR) allele frequency at 95% confidence interval = 0.542 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
ENSG00000287973	ENST00000720812.1	n.118+12414C>G		intron_variant	Intron 1 of 3
ENSG00000287973	ENST00000720813.1	n.90+12414C>G		intron_variant	Intron 1 of 3
ENSG00000287973	ENST00000720814.1	n.127+12414C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70265 AN: 151854 Hom.: 17311 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.463 AC: 70314 AN: 151972 Hom.: 17327 Cov.: 31 AF XY: 0.467 AC XY: 34710 AN XY: 74274

African (AFR) AF: 0.309 AC: 12813 AN: 41454

American (AMR) AF: 0.552 AC: 8428 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1916 AN: 3466

East Asian (EAS) AF: 0.229 AC: 1180 AN: 5164

South Asian (SAS) AF: 0.501 AC: 2411 AN: 4814

European-Finnish (FIN) AF: 0.614 AC: 6492 AN: 10566

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35501 AN: 67924

Other (OTH) AF: 0.463 AC: 977 AN: 2108

Alfa AF: 0.348 Hom.: 984

Bravo AF: 0.452

Asia WGS AF: 0.385 AC: 1339 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	0.28
DANN	Benign	0.27
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1820450; hg19: chr15-34893264;