chr14-39444622-T-A

Position:

• chr14-39444622-T-A

Variant summary

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

The ENST00000652126.1(ENSG00000258526):​n.69+11947T>A 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 0.613 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: ENST00000652126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105370461	XR_001750723.2	n.83+12191T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652126.1	n.69+11947T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.635

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332387; hg19: chr14-39913826;