rs1030154

chr5-165624325-G-A

Variant summary

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

The ENST00000522189.1(ENSG00000253693):n.22-153652G>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 0.195 in 152,014 control chromosomes in the GnomAD database, including 3,067 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 0.19 (3067 hom., cov: 32)
• Consequence: ENST00000522189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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
	ENST00000522189.1	n.22-153652G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29551 AN: 151894 Hom.: 3063 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.195 AC: 29585 AN: 152014 Hom.: 3067 Cov.: 32 AF XY: 0.201 AC XY: 14924 AN XY: 74268

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.185

Alfa AF: 0.189 Hom.: 5561

Bravo AF: 0.187

Asia WGS AF: 0.271 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1030154; hg19: chr5-165051330;