rs514049

Positions:

• chr15-58750164-C-A
• chr15-58750164-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000671030.1(ENSG00000286897):​n.213+29C>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 0.573 in 152,170 control chromosomes in the GnomAD database, including 27,694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.57 (27694 hom., cov: 33)
• Consequence: ENST00000671030.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.120

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 15-58750164-C-A is Benign according to our data. Variant chr15-58750164-C-A is described in ClinVar as [Benign]. Clinvar id is 1233353.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000671030.1	n.213+29C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87074 AN: 152052 Hom.: 27638 Cov.: 33

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.573 AC: 87193 AN: 152170 Hom.: 27694 Cov.: 33 AF XY: 0.582 AC XY: 43304 AN XY: 74398

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.526

Alfa AF: 0.482 Hom.: 6979

Bravo AF: 0.586

Asia WGS AF: 0.771 AC: 2677 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs514049; hg19: chr15-59042363;