rs7328488

Variant names:

• chr13-85698523-C-A
• rs7328488
• ENST00000647840.1:n.628+293G>T

Variant summary

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

The ENST00000647840.1(ENSG00000285834):​n.628+293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0486 in 152,136 control chromosomes in the GnomAD database, including 255 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 0.049 (255 hom., cov: 32)
• Consequence: ENSG00000285834 ENST00000647840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808
• Publications: 1 publications found

Genes affected

ENSG00000285834 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0906 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
ENSG00000285834	ENST00000647840.1	n.628+293G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0487 AC: 7398 AN: 152018 Hom.: 254 Cov.: 32

Gnomad AFR AF: 0.0932

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0295

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0486 AC: 7397 AN: 152136 Hom.: 255 Cov.: 32 AF XY: 0.0471 AC XY: 3505 AN XY: 74376

African (AFR) AF: 0.0931 AC: 3862 AN: 41494

American (AMR) AF: 0.0422 AC: 644 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3472

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5158

South Asian (SAS) AF: 0.0790 AC: 380 AN: 4808

European-Finnish (FIN) AF: 0.0105 AC: 111 AN: 10596

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0295 AC: 2008 AN: 68014

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0387 Hom.: 309

Bravo AF: 0.0504

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.61
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs7328488; hg19: chr13-86272658;