chr5-1345966-T-C

Position:

• chr5-1345966-T-C

Variant summary

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

The ENST00000656081.1(ENSG00000286388):​n.770T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,150 control chromosomes in the GnomAD database, including 5,633 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 0.27 (5633 hom., cov: 33)
• Consequence: ENSG00000286388 ENST00000656081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

ENSG00000286388 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1345966T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286388	ENST00000656081.1	n.770T>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40305 AN: 152032 Hom.: 5631 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.265 AC: 40338 AN: 152150 Hom.: 5633 Cov.: 33 AF XY: 0.258 AC XY: 19196 AN XY: 74396

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.250

Alfa AF: 0.256 Hom.: 1221

Bravo AF: 0.271

Asia WGS AF: 0.148 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27071; hg19: chr5-1346081;