15-37383382-C-T

Position:

• chr15-37383382-C-T

Variant summary

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

The ENST00000663330.1(ENSG00000259434):​n.242-16280G>A 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 0.541 in 151,240 control chromosomes in the GnomAD database, including 23,127 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 0.54 (23127 hom., cov: 28)
• Consequence: ENST00000663330.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370772	XR_932115.3	n.221-16280G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663330.1	n.242-16280G>A		intron_variant, non_coding_transcript_variant
	ENST00000561054.2	n.314-16280G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000669587.1	n.388-16280G>A		intron_variant, non_coding_transcript_variant
	ENST00000669775.1	n.253-16280G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.541 AC: 81753 AN: 151122 Hom.: 23105 Cov.: 28

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.541 AC: 81825 AN: 151240 Hom.: 23127 Cov.: 28 AF XY: 0.541 AC XY: 39983 AN XY: 73858

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.500

Alfa AF: 0.481 Hom.: 10116

Bravo AF: 0.544

Asia WGS AF: 0.484 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs603165; hg19: chr15-37675583;