chr20-43476299-C-A

Variant names:

• chr20-43476299-C-A
• rs4812712
• ENST00000657241.1:c.653+15701C>A

Variant summary

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

The ENST00000657241.1(ENSG00000288000):​c.653+15701C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,076 control chromosomes in the GnomAD database, including 11,265 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 0.34 (11265 hom., cov: 32)
• Consequence: ENSG00000288000 ENST00000657241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 5 publications found

Genes affected

ENSG00000288000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

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
ENSG00000288000	ENST00000657241.1	c.653+15701C>A		intron_variant	Intron 5 of 25			ENSP00000499734.1
ENSG00000295152	ENST00000728295.1	n.168+3730G>T		intron_variant	Intron 1 of 1
ENSG00000295152	ENST00000728296.1	n.134+3730G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51657 AN: 151958 Hom.: 11228 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.340 AC: 51762 AN: 152076 Hom.: 11265 Cov.: 32 AF XY: 0.339 AC XY: 25214 AN XY: 74342

African (AFR) AF: 0.616 AC: 25522 AN: 41458

American (AMR) AF: 0.350 AC: 5355 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3468

East Asian (EAS) AF: 0.143 AC: 743 AN: 5186

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2893 AN: 10566

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14482 AN: 67984

Other (OTH) AF: 0.285 AC: 601 AN: 2106

Alfa AF: 0.252 Hom.: 17203

Bravo AF: 0.357

Asia WGS AF: 0.280 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.67
DANN	Benign	0.73
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4812712; hg19: chr20-42104939;