rs4924346

Positions:

• chr15-39347791-G-A
• chr15-39347791-G-T

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.67+73118C>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 0.0909 in 152,058 control chromosomes in the GnomAD database, including 634 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 0.091 (634 hom., cov: 32)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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 (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+72753C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560484.1	n.67+73118C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000558209.1	n.451+11998C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000559318.1	n.409-48309C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13820 AN: 151938 Hom.: 635 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.0897

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0835

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

GnomAD4 genome AF: 0.0909 AC: 13825 AN: 152058 Hom.: 634 Cov.: 32 AF XY: 0.0897 AC XY: 6670 AN XY: 74336

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.0911

Gnomad4 EAS AF: 0.0418

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.0830

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.0845

Alfa AF: 0.0435 Hom.: 35

Bravo AF: 0.0907

Asia WGS AF: 0.0720 AC: 250 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	2.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4924346; hg19: chr15-39639992;