rs1520954

chr15-37417952-A-G

Variant summary

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

The ENST00000663330.1(ENSG00000259434):n.241+2108T>C 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 0.485 in 151,996 control chromosomes in the GnomAD database, including 18,286 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 0.48 (18286 hom., cov: 32)
• Consequence: ENST00000663330.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370772	XR_932115.3	n.220+2108T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663330.1	n.241+2108T>C		intron_variant, non_coding_transcript_variant
	ENST00000561054.2	n.313+2108T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000669587.1	n.387+1488T>C		intron_variant, non_coding_transcript_variant
	ENST00000669775.1	n.252+2108T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73638 AN: 151878 Hom.: 18266 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.485 AC: 73699 AN: 151996 Hom.: 18286 Cov.: 32 AF XY: 0.474 AC XY: 35246 AN XY: 74292

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.519

Alfa AF: 0.519 Hom.: 8368

Bravo AF: 0.499

Asia WGS AF: 0.319 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.36
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1520954; hg19: chr15-37710153;