rs9327930

chr5-105188370-A-Gchr5-105188370-A-T

Variant summary

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

The ENST00000503650.1(ENSG00000251574):n.210+204391T>C 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 0.329 in 151,694 control chromosomes in the GnomAD database, including 9,540 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 0.33 (9540 hom., cov: 31)
• Consequence: ENST00000503650.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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
	ENST00000503650.1	n.210+204391T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000522464.1	n.68+57927T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49898 AN: 151576 Hom.: 9515 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.329 AC: 49973 AN: 151694 Hom.: 9540 Cov.: 31 AF XY: 0.330 AC XY: 24447 AN XY: 74106

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.330

Alfa AF: 0.249 Hom.: 8957

Bravo AF: 0.351

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.68
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327930; hg19: chr5-104524071;