5-51525504-A-T

Variant summary

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

The ENST00000666280.1(ENSG00000288035):n.436-40644T>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 0.467 in 150,536 control chromosomes in the GnomAD database, including 16,890 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 0.47 (16890 hom., cov: 32)
• Consequence: ENST00000666280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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
	ENST00000666280.1	n.436-40644T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70215 AN: 150418 Hom.: 16862 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.467 AC: 70301 AN: 150536 Hom.: 16890 Cov.: 32 AF XY: 0.461 AC XY: 33901 AN XY: 73496

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.432

Alfa AF: 0.460 Hom.: 2051

Bravo AF: 0.470

Asia WGS AF: 0.352 AC: 1221 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.5
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs986714; hg19: chr5-50821338;