chr5-155127535-A-G

Position:

• chr5-155127535-A-G

Variant summary

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

The ENST00000660390.1(ENSG00000287963):​n.281+39825A>G 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 0.217 in 152,196 control chromosomes in the GnomAD database, including 4,019 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 0.22 (4019 hom., cov: 33)
• Consequence: ENST00000660390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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
	ENST00000660390.1	n.281+39825A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32900 AN: 152078 Hom.: 4002 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00866

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.217 AC: 32955 AN: 152196 Hom.: 4019 Cov.: 33 AF XY: 0.214 AC XY: 15919 AN XY: 74428

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.00868

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.193

Alfa AF: 0.203 Hom.: 788

Bravo AF: 0.214

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6882113; hg19: chr5-154507095;