chr20-43476841-A-G

Variant names:

• chr20-43476841-A-G
• rs8124813
• ENST00000657241.1:c.653+16243A>G

Variant summary

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

The ENST00000657241.1(ENSG00000288000):​c.653+16243A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,138 control chromosomes in the GnomAD database, including 5,443 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 0.24 (5443 hom., cov: 32)
• Consequence: ENSG00000288000 ENST00000657241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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+16243A>G		intron_variant	Intron 5 of 25			ENSP00000499734.1
ENSG00000295152	ENST00000728295.1	n.168+3188T>C		intron_variant	Intron 1 of 1
ENSG00000295152	ENST00000728296.1	n.134+3188T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35885 AN: 152020 Hom.: 5448 Cov.: 32

Gnomad AFR AF: 0.0617

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.236 AC: 35876 AN: 152138 Hom.: 5443 Cov.: 32 AF XY: 0.234 AC XY: 17364 AN XY: 74358

African (AFR) AF: 0.0616 AC: 2559 AN: 41536

American (AMR) AF: 0.212 AC: 3241 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3472

East Asian (EAS) AF: 0.119 AC: 617 AN: 5176

South Asian (SAS) AF: 0.152 AC: 733 AN: 4824

European-Finnish (FIN) AF: 0.306 AC: 3231 AN: 10570

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23638 AN: 67964

Other (OTH) AF: 0.244 AC: 514 AN: 2108

Alfa AF: 0.304 Hom.: 4218

Bravo AF: 0.220

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.39
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs8124813; hg19: chr20-42105481;