rs16893872

Variant names:

• chr5-24729897-C-T
• rs16893872
• ENST00000662665.2:n.201+397C>T

Variant summary

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

The ENST00000662665.2(ENSG00000286454):​n.201+397C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,214 control chromosomes in the GnomAD database, including 685 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 0.057 (685 hom., cov: 31)
• Consequence: ENSG00000286454 ENST00000662665.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 3 publications found

Genes affected

ENSG00000286454 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662665.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286454	ENST00000662665.2		n.201+397C>T		intron	N/A
	ENSG00000286454	ENST00000814888.1		n.219-5456C>T		intron	N/A
	ENSG00000286454	ENST00000814889.1		n.636+2294C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8576 AN: 152096 Hom.: 678 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0116

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00966

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0565 AC: 8601 AN: 152214 Hom.: 685 Cov.: 31 AF XY: 0.0547 AC XY: 4074 AN XY: 74418

African (AFR) AF: 0.177 AC: 7355 AN: 41496

American (AMR) AF: 0.0282 AC: 432 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0116 AC: 40 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00414 AC: 20 AN: 4832

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10612

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00966 AC: 657 AN: 68022

Other (OTH) AF: 0.0407 AC: 86 AN: 2112

Alfa AF: 0.0258 Hom.: 111

Bravo AF: 0.0635

Asia WGS AF: 0.00953 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs16893872; hg19: chr5-24730006;