ENST00000650911.1:n.29+11947T>A

Variant names:

• chr14-39444622-T-A
• rs9332387
• ENST00000650911.1:n.29+11947T>A

Variant summary

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

The ENST00000650911.1(ENSG00000258526):​n.29+11947T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,002 control chromosomes in the GnomAD database, including 31,231 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 0.61 (31231 hom., cov: 31)
• Consequence: ENSG00000258526 ENST00000650911.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 2 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370461	XR_001750719.2	n.64+11947T>A		intron_variant	Intron 1 of 4
LOC105370461	XR_001750723.2	n.83+12191T>A		intron_variant	Intron 1 of 4
LOC105370461	XR_001750725.1	n.81+12103T>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258526	ENST00000650911.1	n.29+11947T>A		intron_variant	Intron 1 of 5
ENSG00000258526	ENST00000650949.2	n.77+11947T>A		intron_variant	Intron 1 of 2
ENSG00000258526	ENST00000651829.1	n.64+11947T>A		intron_variant	Intron 1 of 13

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93207 AN: 151884 Hom.: 31217 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.613 AC: 93252 AN: 152002 Hom.: 31231 Cov.: 31 AF XY: 0.618 AC XY: 45935 AN XY: 74318

African (AFR) AF: 0.332 AC: 13748 AN: 41428

American (AMR) AF: 0.684 AC: 10441 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2150 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2498 AN: 5138

South Asian (SAS) AF: 0.780 AC: 3760 AN: 4820

European-Finnish (FIN) AF: 0.784 AC: 8284 AN: 10566

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50229 AN: 67990

Other (OTH) AF: 0.635 AC: 1344 AN: 2116

Alfa AF: 0.670 Hom.: 4489

Bravo AF: 0.591

Asia WGS AF: 0.607 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.35
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs9332387; hg19: chr14-39913826;