14-39444622-T-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650911.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258526	ENST00000650911.1		n.29+11947T>A		intron	N/A
	ENSG00000258526	ENST00000650949.2		n.77+11947T>A		intron	N/A
	ENSG00000258526	ENST00000651829.1		n.64+11947T>A		intron	N/A

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 v4.9

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;