chr5-91778169-T-A

Position:

• chr5-91778169-T-A

Variant summary

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

The ENST00000651690.1(ENSG00000286121):​n.459-5688T>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 0.698 in 151,994 control chromosomes in the GnomAD database, including 37,522 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 0.70 (37522 hom., cov: 32)
• Consequence: ENST00000651690.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651690.1	n.459-5688T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105955 AN: 151876 Hom.: 37470 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.698 AC: 106062 AN: 151994 Hom.: 37522 Cov.: 32 AF XY: 0.695 AC XY: 51613 AN XY: 74288

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.677

Alfa AF: 0.598 Hom.: 1856

Bravo AF: 0.702

Asia WGS AF: 0.608 AC: 2108 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2939244; hg19: chr5-91073986;