14-64386958-A-G

Variant summary

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

The ENST00000641479.1(ENSG00000293482):n.570+459T>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 0.553 in 152,110 control chromosomes in the GnomAD database, including 25,780 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 0.55 (25777 hom., cov: 32)
  • Exomes 𝑓: 0.40 (3 hom.)
• Consequence: ENST00000641479.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641479.1	n.570+459T>C		intron_variant, non_coding_transcript_variant
	ENST00000641725.1	n.96T>C		non_coding_transcript_exon_variant	1/6
	ENST00000689962.1	n.982T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84077 AN: 151942 Hom.: 25738 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.400 AC: 20 AN: 50 Hom.: 3 Cov.: 0 AF XY: 0.405 AC XY: 17 AN XY: 42

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.381

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.554 AC: 84171 AN: 152060 Hom.: 25777 Cov.: 32 AF XY: 0.544 AC XY: 40407 AN XY: 74322

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.535

Alfa AF: 0.341 Hom.: 904

Bravo AF: 0.576

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8010584; hg19: chr14-64853676;