chr5-51525504-A-T

Variant names:

• chr5-51525504-A-T
• rs986714
• ENST00000666280.1:n.436-40644T>A

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 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: ENSG00000288035 ENST00000666280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

ENSG00000288035 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288035	ENST00000666280.1	n.436-40644T>A		intron_variant	Intron 1 of 3

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;