ENST00000652447.1:n.87+11573A>G

Variant names:

• chr20-4673489-T-C
• rs16989992
• ENST00000652447.1:n.87+11573A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000652447.1(ENSG00000293214):​n.87+11573A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0192 in 152,256 control chromosomes in the GnomAD database, including 35 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 0.019 (35 hom., cov: 32)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 0 publications found

Genes affected

ENSG00000293214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0192 (2929/152256) while in subpopulation SAS AF = 0.0305 (147/4820). AF 95% confidence interval is 0.0265. There are 35 homozygotes in GnomAd4. There are 1446 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 35 gene

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
ENSG00000293214	ENST00000652447.1	n.87+11573A>G		intron_variant	Intron 1 of 1
ENSG00000293214	ENST00000773443.1	n.131+75A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0193 AC: 2931 AN: 152138 Hom.: 35 Cov.: 32

Gnomad AFR AF: 0.00442

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0134

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

GnomAD4 genome AF: 0.0192 AC: 2929 AN: 152256 Hom.: 35 Cov.: 32 AF XY: 0.0194 AC XY: 1446 AN XY: 74442

African (AFR) AF: 0.00440 AC: 183 AN: 41548

American (AMR) AF: 0.0111 AC: 169 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4820

European-Finnish (FIN) AF: 0.0486 AC: 515 AN: 10602

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0267 AC: 1814 AN: 68032

Other (OTH) AF: 0.0133 AC: 28 AN: 2112

Alfa AF: 0.0245 Hom.: 48

Bravo AF: 0.0160

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.68
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs16989992; hg19: chr20-4654135;