rs10518280

Variant names:

• chr19-23872279-A-C
• rs10518280
• ENST00000599944.1:n.150+2273T>G

Variant summary

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

The ENST00000599944.1(ENSG00000267924):​n.150+2273T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,192 control chromosomes in the GnomAD database, including 1,105 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 0.12 (1105 hom., cov: 31)
• Consequence: ENSG00000267924 ENST00000599944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 1 publications found

Genes affected

ENSG00000267924 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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
ENSG00000267924	ENST00000599944.1	n.150+2273T>G		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17861 AN: 152072 Hom.: 1105 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.117 AC: 17869 AN: 152192 Hom.: 1105 Cov.: 31 AF XY: 0.116 AC XY: 8650 AN XY: 74422

African (AFR) AF: 0.121 AC: 5043 AN: 41510

American (AMR) AF: 0.0847 AC: 1295 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5170

South Asian (SAS) AF: 0.147 AC: 707 AN: 4820

European-Finnish (FIN) AF: 0.0854 AC: 907 AN: 10618

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 7999 AN: 68006

Other (OTH) AF: 0.114 AC: 240 AN: 2112

Alfa AF: 0.115 Hom.: 551

Bravo AF: 0.117

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	14
DANN	Benign	0.55
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10518280; hg19: chr19-24055081;