chr5-1345359-A-G

Position:

• chr5-1345359-A-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: ENST00000656081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

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 = 0.705 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
	ENST00000656081.1	n.163A>G		non_coding_transcript_exon_variant	1/2

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;