rs10147986

Variant names:

• chr14-51756077-A-C
• rs10147986
• ENST00000557308.1:n.216-5030A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-51756077-A-C
• chr14-51756077-A-G
• chr14-51756077-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557308.1(ENSG00000259111):​n.216-5030A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 151,724 control chromosomes in the GnomAD database, including 42,929 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 0.75 (42929 hom., cov: 32)
• Consequence: ENSG00000259111 ENST00000557308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 1 publications found

Genes affected

ENSG00000259111 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.12).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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
ENSG00000259111	ENST00000557308.1	n.216-5030A>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113534 AN: 151602 Hom.: 42896 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.749 AC: 113624 AN: 151724 Hom.: 42929 Cov.: 32 AF XY: 0.757 AC XY: 56159 AN XY: 74168

African (AFR) AF: 0.664 AC: 27354 AN: 41190

American (AMR) AF: 0.821 AC: 12506 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5140 AN: 5166

South Asian (SAS) AF: 0.742 AC: 3575 AN: 4820

European-Finnish (FIN) AF: 0.810 AC: 8582 AN: 10590

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51515 AN: 67940

Other (OTH) AF: 0.751 AC: 1583 AN: 2108

Alfa AF: 0.720 Hom.: 3342

Bravo AF: 0.751

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.82
DANN	Benign	0.085
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10147986; hg19: chr14-52222795;