chr5-155132321-G-A

Position:

• chr5-155132321-G-A

Variant summary

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

The ENST00000660390.1(ENSG00000287963):​n.281+44611G>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 0.217 in 152,164 control chromosomes in the GnomAD database, including 4,055 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 (4055 hom., cov: 33)
• Consequence: ENST00000660390.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

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 = 0.33 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+44611G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33024 AN: 152048 Hom.: 4039 Cov.: 33

Gnomad AFR AF: 0.334

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: 0.199

Gnomad MID AF: 0.187

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: 33079 AN: 152164 Hom.: 4055 Cov.: 33 AF XY: 0.215 AC XY: 15973 AN XY: 74392

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.00868

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.192

Alfa AF: 0.189 Hom.: 5871

Bravo AF: 0.215

Asia WGS AF: 0.116 AC: 405 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	12
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6866348; hg19: chr5-154511881;