10-45008431-C-T

Variant summary

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

The ENST00000456938.6(ENSG00000293022):n.619-4356G>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 0.487 in 152,076 control chromosomes in the GnomAD database, including 20,367 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 0.49 (20367 hom., cov: 33)
• Consequence: ENST00000456938.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 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
	ENST00000456938.6	n.619-4356G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74125 AN: 151958 Hom.: 20365 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.487 AC: 74130 AN: 152076 Hom.: 20367 Cov.: 33 AF XY: 0.491 AC XY: 36499 AN XY: 74344

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.506

Alfa AF: 0.410 Hom.: 1274

Bravo AF: 0.467

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.2
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2210497; hg19: chr10-45503879;