rs514049

Variant names:

• chr15-58750164-C-A
• rs514049
• ENST00000671030.1:n.213+29C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000671030.1(ENSG00000286897):​n.213+29C>A variant causes a intron 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: ENSG00000286897 ENST00000671030.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.120
• Publications: 25 publications found

Genes affected

ENSG00000286897 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286897	ENST00000671030.1	n.213+29C>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.822 AC: 34168 AN: 41544

American (AMR) AF: 0.555 AC: 8481 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1484 AN: 3472

East Asian (EAS) AF: 0.936 AC: 4841 AN: 5174

South Asian (SAS) AF: 0.612 AC: 2954 AN: 4826

European-Finnish (FIN) AF: 0.555 AC: 5871 AN: 10576

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27765 AN: 67962

Other (OTH) AF: 0.526 AC: 1112 AN: 2116

Alfa AF: 0.484 Hom.: 8454

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

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.9
DANN	Benign	0.58
PhyloP100		-0.12
PromoterAI		-0.14	Neutral

Splicing

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

Other links and lift over

dbSNP: rs514049; hg19: chr15-59042363;