rs3827143

Variant names:

• chr20-23638980-A-G
• rs3827143
• ENST00000801340.1:n.120+1470A>G

Variant summary

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

The ENST00000801340.1(ENSG00000286117):​n.120+1470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,136 control chromosomes in the GnomAD database, including 3,324 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 0.20 (3324 hom., cov: 32)
• Consequence: ENSG00000286117 ENST00000801340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 17 publications found

Genes affected

ENSG00000286117 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 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
ENSG00000286117	ENST00000801340.1	n.120+1470A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30834 AN: 152018 Hom.: 3324 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.203 AC: 30842 AN: 152136 Hom.: 3324 Cov.: 32 AF XY: 0.204 AC XY: 15141 AN XY: 74380

African (AFR) AF: 0.214 AC: 8882 AN: 41474

American (AMR) AF: 0.133 AC: 2041 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3470

East Asian (EAS) AF: 0.122 AC: 629 AN: 5176

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4820

European-Finnish (FIN) AF: 0.228 AC: 2415 AN: 10598

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14270 AN: 67992

Other (OTH) AF: 0.186 AC: 392 AN: 2106

Alfa AF: 0.200 Hom.: 7520

Bravo AF: 0.190

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3827143; hg19: chr20-23619617;