rs16997087

Variant names:

• chr20-16074337-T-C
• rs16997087
• ENST00000721848.1:n.194-14310A>G

Variant summary

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

The ENST00000721848.1(ENSG00000294201):​n.194-14310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0525 in 152,296 control chromosomes in the GnomAD database, including 272 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 0.052 (272 hom., cov: 32)
• Consequence: ENSG00000294201 ENST00000721848.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 5 publications found

Genes affected

ENSG00000294201 (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 (EAS) allele frequency at 95% confidence interval = 0.0823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721848.1. 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
	ENSG00000294201	ENST00000721848.1		n.194-14310A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 8001 AN: 152178 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0597

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

GnomAD4 genome AF: 0.0525 AC: 7995 AN: 152296 Hom.: 272 Cov.: 32 AF XY: 0.0537 AC XY: 4002 AN XY: 74482

African (AFR) AF: 0.0143 AC: 594 AN: 41570

American (AMR) AF: 0.0595 AC: 910 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3470

East Asian (EAS) AF: 0.0890 AC: 462 AN: 5190

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4824

European-Finnish (FIN) AF: 0.0938 AC: 995 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4280 AN: 68016

Other (OTH) AF: 0.0586 AC: 124 AN: 2116

Alfa AF: 0.0598 Hom.: 516

Bravo AF: 0.0487

Asia WGS AF: 0.0920 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.52
PhyloP100		-0.43

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16997087;

hg19: chr20-16054982;