rs591323

Variant names:

• chr8-16839582-G-A
• rs591323
• ENST00000521411.2:n.278+4523C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-16839582-G-A
• chr8-16839582-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521411.2(ENSG00000253496):​n.278+4523C>T variant causes a intron 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: ENSG00000253496 ENST00000521411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 44 publications found

Genes affected

ENSG00000253496 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105379297	XR_949525.1	n.158-56300C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253496	ENST00000521411.2	n.278+4523C>T		intron_variant	Intron 2 of 3	5
ENSG00000253496	ENST00000755781.1	n.229-56300C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.276 AC: 11462 AN: 41462

American (AMR) AF: 0.298 AC: 4534 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3464

East Asian (EAS) AF: 0.417 AC: 2145 AN: 5146

South Asian (SAS) AF: 0.518 AC: 2489 AN: 4806

European-Finnish (FIN) AF: 0.335 AC: 3537 AN: 10554

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19007 AN: 67944

Other (OTH) AF: 0.276 AC: 581 AN: 2104

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs591323; hg19: chr8-16697091;