rs1520961

chr15-37444454-G-A

Variant summary

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

The ENST00000663330.1(ENSG00000259434):n.116-24269C>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 0.25 in 151,856 control chromosomes in the GnomAD database, including 4,968 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 (4968 hom., cov: 32)
• Consequence: ENST00000663330.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 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
	ENST00000663330.1	n.116-24269C>T		intron_variant, non_coding_transcript_variant
	ENST00000561054.2	n.89-17692C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000669587.1	n.127-24269C>T		intron_variant, non_coding_transcript_variant
	ENST00000669775.1	n.127-24269C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37915 AN: 151736 Hom.: 4973 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.368

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.250 AC: 37916 AN: 151856 Hom.: 4968 Cov.: 32 AF XY: 0.247 AC XY: 18303 AN XY: 74228

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.270

Alfa AF: 0.275 Hom.: 780

Bravo AF: 0.248

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.31
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1520961; hg19: chr15-37736655;