rs10147986

Positions:

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

Variant summary

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

The ENST00000557308.1(ENSG00000259111):​n.216-5030A>C 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 0.749 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: ENST00000557308.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000557308.1	n.216-5030A>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.751

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10147986; hg19: chr14-52222795;