rs4523321

Variant names:

• chr9-101775328-C-T
• rs4523321
• ENST00000764873.1:n.414-19278C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000764873.1(ENSG00000299588):​n.414-19278C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 151,950 control chromosomes in the GnomAD database, including 61 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 0.015 (61 hom., cov: 32)
• Consequence: ENSG00000299588 ENST00000764873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 2 publications found

Genes affected

ENSG00000299588 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0148 (2254/151950) while in subpopulation AFR AF = 0.0511 (2119/41488). AF 95% confidence interval is 0.0493. There are 61 homozygotes in GnomAd4. There are 1037 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 61 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299588	ENST00000764873.1	n.414-19278C>T		intron_variant	Intron 4 of 4
ENSG00000299588	ENST00000764874.1	n.248-19278C>T		intron_variant	Intron 3 of 3
ENSG00000299588	ENST00000764877.1	n.263-19278C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 2237 AN: 151832 Hom.: 60 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00545

Gnomad ASJ AF: 0.00462

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00957

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

GnomAD4 genome AF: 0.0148 AC: 2254 AN: 151950 Hom.: 61 Cov.: 32 AF XY: 0.0140 AC XY: 1037 AN XY: 74312

African (AFR) AF: 0.0511 AC: 2119 AN: 41488

American (AMR) AF: 0.00551 AC: 84 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00462 AC: 16 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000162 AC: 11 AN: 67810

Other (OTH) AF: 0.00947 AC: 20 AN: 2112

Alfa AF: 0.0147 Hom.: 14

Bravo AF: 0.0168

Asia WGS AF: 0.00434 AC: 15 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.098
DANN	Benign	0.34
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4523321; hg19: chr9-104537610;