rs4528684

Variant names:

• chr19-14240762-C-T
• rs4528684
• ENST00000715974.1:n.688-5591G>A

Variant summary

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

The ENST00000715974.1(ENSG00000267723):​n.688-5591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,176 control chromosomes in the GnomAD database, including 1,294 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 0.12 (1294 hom., cov: 32)
• Consequence: ENSG00000267723 ENST00000715974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 9 publications found

Genes affected

ENSG00000267723 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

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
ENSG00000267723	ENST00000715974.1	n.688-5591G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17915 AN: 152058 Hom.: 1291 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0666

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.118 AC: 17935 AN: 152176 Hom.: 1294 Cov.: 32 AF XY: 0.116 AC XY: 8611 AN XY: 74412

African (AFR) AF: 0.202 AC: 8388 AN: 41512

American (AMR) AF: 0.0746 AC: 1138 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3470

East Asian (EAS) AF: 0.0451 AC: 233 AN: 5172

South Asian (SAS) AF: 0.0658 AC: 318 AN: 4834

European-Finnish (FIN) AF: 0.0940 AC: 997 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0930 AC: 6328 AN: 68010

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.0966 Hom.: 3298

Bravo AF: 0.118

Asia WGS AF: 0.0770 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.87
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4528684; hg19: chr19-14351574;