5-1345359-A-G

Variant names:

• chr5-1345359-A-G
• rs27996
• ENST00000656081.1:n.163A>G

Variant summary

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

The ENST00000656081.1(ENSG00000286388):​n.163A>G 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 0.487 in 152,044 control chromosomes in the GnomAD database, including 19,842 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 (19842 hom., cov: 33)
• Consequence: ENSG00000286388 ENST00000656081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

ENSG00000286388 (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 = 0.705 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
ENSG00000286388	ENST00000656081.1	n.163A>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74056 AN: 151934 Hom.: 19822 Cov.: 33

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.487 AC: 74120 AN: 152044 Hom.: 19842 Cov.: 33 AF XY: 0.478 AC XY: 35508 AN XY: 74338

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.458

Alfa AF: 0.389 Hom.: 2353

Bravo AF: 0.494

Asia WGS AF: 0.237 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.86
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27996; hg19: chr5-1345474;