rs10491468

chr5-120250961-G-C

Variant summary

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

The ENST00000514240.1(ENSG00000251293):n.248-5328C>G 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 0.216 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: ENST00000514240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000514240.1	n.248-5328C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.224

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491468; hg19: chr5-119586656;