chr20-40753199-G-A

Variant names:

• chr20-40753199-G-A
• rs1883701
• ENST00000655799.1:n.324-3882G>A

Variant summary

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

The ENST00000655799.1(ENSG00000286972):​n.324-3882G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 152,232 control chromosomes in the GnomAD database, including 186 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 0.017 (186 hom., cov: 32)
• Consequence: ENSG00000286972 ENST00000655799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 1 publications found

Genes affected

ENSG00000286972 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655799.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286972	ENST00000655799.1		n.324-3882G>A		intron	N/A
	ENSG00000229771	ENST00000758964.1		n.168+24863C>T		intron	N/A
	ENSG00000298935	ENST00000759166.1		n.75+4007C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 2630 AN: 152112 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.00215

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0123

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.0464

Gnomad FIN AF: 0.00698

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0173 AC: 2632 AN: 152232 Hom.: 186 Cov.: 32 AF XY: 0.0191 AC XY: 1425 AN XY: 74414

African (AFR) AF: 0.00214 AC: 89 AN: 41564

American (AMR) AF: 0.0127 AC: 194 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5168

South Asian (SAS) AF: 0.0465 AC: 224 AN: 4820

European-Finnish (FIN) AF: 0.00698 AC: 74 AN: 10604

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00791 AC: 538 AN: 68022

Other (OTH) AF: 0.0161 AC: 34 AN: 2108

Alfa AF: 0.00855 Hom.: 8

Bravo AF: 0.0182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1883701; hg19: chr20-39381839;