rs591323

chr8-16839582-G-Achr8-16839582-G-C

Variant summary

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

The ENST00000521411.2(ENSG00000253496):n.278+4523C>T 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 0.296 in 151,918 control chromosomes in the GnomAD database, including 6,932 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 0.30 (6932 hom., cov: 31)
• Consequence: ENST00000521411.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379297	XR_949525.1	n.158-56300C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521411.2	n.278+4523C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44912 AN: 151800 Hom.: 6930 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.296 AC: 44942 AN: 151918 Hom.: 6932 Cov.: 31 AF XY: 0.306 AC XY: 22746 AN XY: 74244

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.276

Alfa AF: 0.226 Hom.: 1144

Bravo AF: 0.288

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.39
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs591323; hg19: chr8-16697091;