rs359457

Variant names:

• chr5-173852839-C-T
• rs359457
• ENST00000732368.1:n.272+19507C>T

Variant summary

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

The ENST00000732368.1(ENSG00000287003):​n.272+19507C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,922 control chromosomes in the GnomAD database, including 26,304 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 0.58 (26304 hom., cov: 31)
• Consequence: ENSG00000287003 ENST00000732368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 49 publications found

Genes affected

ENSG00000287003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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
ENSG00000287003	ENST00000732368.1	n.272+19507C>T		intron_variant	Intron 2 of 2
ENSG00000295760	ENST00000732588.1	n.140-6934G>A		intron_variant	Intron 1 of 2
ENSG00000295760	ENST00000732589.1	n.86+661G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88533 AN: 151804 Hom.: 26280 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.583 AC: 88601 AN: 151922 Hom.: 26304 Cov.: 31 AF XY: 0.577 AC XY: 42827 AN XY: 74190

African (AFR) AF: 0.681 AC: 28216 AN: 41426

American (AMR) AF: 0.472 AC: 7210 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2008 AN: 3466

East Asian (EAS) AF: 0.391 AC: 2016 AN: 5156

South Asian (SAS) AF: 0.615 AC: 2957 AN: 4810

European-Finnish (FIN) AF: 0.510 AC: 5371 AN: 10530

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38656 AN: 67950

Other (OTH) AF: 0.624 AC: 1315 AN: 2108

Alfa AF: 0.571 Hom.: 115299

Bravo AF: 0.581

Asia WGS AF: 0.561 AC: 1951 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.70
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs359457; hg19: chr5-173279842; COSMIC: COSV60233946;