rs10491468

Variant names:

• chr5-120250961-G-C
• rs10491468
• ENST00000514240.1:n.248-5328C>G

Variant summary

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

The ENST00000514240.1(ENSG00000251293):​n.248-5328C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,694 control chromosomes in the GnomAD database, including 3,834 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 0.22 (3834 hom., cov: 32)
• Consequence: ENSG00000251293 ENST00000514240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 2 publications found

Genes affected

ENSG00000251293 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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
ENSG00000251293	ENST00000514240.1	n.248-5328C>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32677 AN: 151576 Hom.: 3824 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.216 AC: 32725 AN: 151694 Hom.: 3834 Cov.: 32 AF XY: 0.220 AC XY: 16303 AN XY: 74122

African (AFR) AF: 0.255 AC: 10572 AN: 41432

American (AMR) AF: 0.256 AC: 3881 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3458

East Asian (EAS) AF: 0.413 AC: 2118 AN: 5130

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4820

European-Finnish (FIN) AF: 0.192 AC: 2024 AN: 10554

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11359 AN: 67810

Other (OTH) AF: 0.224 AC: 471 AN: 2104

Alfa AF: 0.197 Hom.: 408

Bravo AF: 0.226

Asia WGS AF: 0.355 AC: 1237 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.2
DANN	Benign	0.69
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10491468; hg19: chr5-119586656;