rs12243558

Variant names:

• chr10-113180743-A-G
• rs12243558
• ENST00000849450.1:n.638+2239A>G

Variant summary

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

The ENST00000849450.1(ENSG00000310382):​n.638+2239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,262 control chromosomes in the GnomAD database, including 10,945 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 0.34 (10945 hom., cov: 34)
• Consequence: ENSG00000310382 ENST00000849450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 1 publications found

Genes affected

ENSG00000310382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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
ENSG00000310382	ENST00000849450.1	n.638+2239A>G		intron_variant	Intron 3 of 3
ENSG00000310382	ENST00000849451.1	n.428+2239A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51296 AN: 152144 Hom.: 10913 Cov.: 34

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.337 AC: 51372 AN: 152262 Hom.: 10945 Cov.: 34 AF XY: 0.335 AC XY: 24975 AN XY: 74464

African (AFR) AF: 0.591 AC: 24552 AN: 41540

American (AMR) AF: 0.304 AC: 4648 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2786 AN: 5178

South Asian (SAS) AF: 0.292 AC: 1411 AN: 4828

European-Finnish (FIN) AF: 0.202 AC: 2148 AN: 10618

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14209 AN: 68002

Other (OTH) AF: 0.316 AC: 667 AN: 2114

Alfa AF: 0.241 Hom.: 8645

Bravo AF: 0.357

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.73
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs12243558; hg19: chr10-114940502;