rs587847

Positions:

• chr15-37367848-C-A

Variant summary

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

The ENST00000663330.1(ENSG00000259434):​n.242-746G>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 0.685 in 151,986 control chromosomes in the GnomAD database, including 36,467 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 0.68 (36467 hom., cov: 31)
• Consequence: ENST00000663330.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

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 = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370772	XR_932115.3	n.221-746G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663330.1	n.242-746G>T		intron_variant, non_coding_transcript_variant
	ENST00000561054.2	n.314-746G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000669587.1	n.388-746G>T		intron_variant, non_coding_transcript_variant
	ENST00000669775.1	n.253-746G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104007 AN: 151868 Hom.: 36428 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.685 AC: 104102 AN: 151986 Hom.: 36467 Cov.: 31 AF XY: 0.681 AC XY: 50602 AN XY: 74280

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.663

Alfa AF: 0.630 Hom.: 14203

Bravo AF: 0.699

Asia WGS AF: 0.628 AC: 2177 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587847; hg19: chr15-37660049;