rs12431815

chr14-39535687-A-G

Variant summary

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

The ENST00000652126.1(ENSG00000258526):n.152+65287A>G 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 0.103 in 152,202 control chromosomes in the GnomAD database, including 1,010 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 0.10 (1010 hom., cov: 32)
• Consequence: ENST00000652126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370461	XR_001750723.2	n.166+65287A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652126.1	n.152+65287A>G		intron_variant, non_coding_transcript_variant
	ENST00000650911.1	n.112+65287A>G		intron_variant, non_coding_transcript_variant
	ENST00000651829.1	n.566+2834A>G		intron_variant, non_coding_transcript_variant
	ENST00000662828.1	n.114+65287A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15698 AN: 152084 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.103 AC: 15693 AN: 152202 Hom.: 1010 Cov.: 32 AF XY: 0.101 AC XY: 7504 AN XY: 74404

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0734

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.0961

Alfa AF: 0.134 Hom.: 2870

Bravo AF: 0.0975

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.025
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12431815; hg19: chr14-40004891;