rs889014

Variant names:

• chr5-173557111-C-T
• rs889014
• ENST00000519821.2:n.312+797C>T

Variant summary

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

The ENST00000519821.2(ENSG00000253768):​n.312+797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,978 control chromosomes in the GnomAD database, including 13,941 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 0.42 (13941 hom., cov: 32)
• Consequence: ENSG00000253768 ENST00000519821.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990
• Publications: 50 publications found

Genes affected

ENSG00000253768 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519821.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253768	ENST00000519821.2	TSL:4	n.312+797C>T		intron	N/A
	ENSG00000253768	ENST00000786989.1		n.*81C>T		downstream_gene	N/A
	ENSG00000253768	ENST00000786990.1		n.*80C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63076 AN: 151860 Hom.: 13910 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.416 AC: 63169 AN: 151978 Hom.: 13941 Cov.: 32 AF XY: 0.415 AC XY: 30855 AN XY: 74276

African (AFR) AF: 0.554 AC: 22972 AN: 41444

American (AMR) AF: 0.424 AC: 6479 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3470

East Asian (EAS) AF: 0.133 AC: 689 AN: 5180

South Asian (SAS) AF: 0.371 AC: 1788 AN: 4814

European-Finnish (FIN) AF: 0.397 AC: 4180 AN: 10534

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24146 AN: 67948

Other (OTH) AF: 0.435 AC: 916 AN: 2104

Alfa AF: 0.370 Hom.: 43299

Bravo AF: 0.420

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.37
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs889014; hg19: chr5-172984114; COSMIC: COSV60233201;