rs2412524

chr15-40501062-G-T

Variant summary

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

The ENST00000561460.5(ENSG00000259536):n.168-7270G>T 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 0.251 in 152,066 control chromosomes in the GnomAD database, including 5,873 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 0.25 (5873 hom., cov: 32)
• Consequence: ENST00000561460.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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
	ENST00000561460.5	n.168-7270G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38193 AN: 151948 Hom.: 5870 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.0860

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.251 AC: 38196 AN: 152066 Hom.: 5873 Cov.: 32 AF XY: 0.256 AC XY: 19031 AN XY: 74300

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.0864

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.263

Alfa AF: 0.296 Hom.: 1289

Bravo AF: 0.227

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.9
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: rs2412524; hg19: chr15-40793261;