chr20-52965533-A-T

Variant names:

• chr20-52965533-A-T
• rs16997358
• ENST00000719647.1:n.52-6998T>A

Variant summary

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

The ENST00000719647.1(ENSG00000293887):​n.52-6998T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,166 control chromosomes in the GnomAD database, including 1,559 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 0.13 (1559 hom., cov: 32)
• Consequence: ENSG00000293887 ENST00000719647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 3 publications found

Genes affected

ENSG00000293887 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719647.1. 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
	ENSG00000293887	ENST00000719647.1		n.52-6998T>A		intron	N/A
	ENSG00000293887	ENST00000719648.1		n.96-6998T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19487 AN: 152048 Hom.: 1553 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0697

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.128 AC: 19507 AN: 152166 Hom.: 1559 Cov.: 32 AF XY: 0.130 AC XY: 9693 AN XY: 74388

African (AFR) AF: 0.177 AC: 7327 AN: 41502

American (AMR) AF: 0.201 AC: 3071 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3468

East Asian (EAS) AF: 0.188 AC: 970 AN: 5168

South Asian (SAS) AF: 0.0693 AC: 335 AN: 4834

European-Finnish (FIN) AF: 0.138 AC: 1458 AN: 10584

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0835 AC: 5680 AN: 68002

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.108 Hom.: 156

Bravo AF: 0.140

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs16997358; hg19: chr20-51582072;