rs4257183

Positions:

• chr15-39349137-C-T

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.67+71772G>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 0.8 in 152,130 control chromosomes in the GnomAD database, including 49,156 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 0.80 (49156 hom., cov: 31)
• Consequence: ENST00000560484.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

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 (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370777	XR_007064588.1	n.517+71407G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000560484.1	n.67+71772G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000558209.1	n.451+10652G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000559318.1	n.409-49655G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121630 AN: 152012 Hom.: 49129 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.800 AC: 121707 AN: 152130 Hom.: 49156 Cov.: 31 AF XY: 0.796 AC XY: 59180 AN XY: 74350

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.811

Alfa AF: 0.850 Hom.: 25139

Bravo AF: 0.782

Asia WGS AF: 0.733 AC: 2548 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.014
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4257183; hg19: chr15-39641338;