chr20-23644910-G-A

Variant names:

• chr20-23644910-G-A
• rs2145231
• ENST00000801340.1:n.120+7400G>A

Variant summary

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

The ENST00000801340.1(ENSG00000286117):​n.120+7400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,032 control chromosomes in the GnomAD database, including 3,256 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 (3256 hom., cov: 32)
• Consequence: ENSG00000286117 ENST00000801340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 14 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801340.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286117	ENST00000801340.1		n.120+7400G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29633 AN: 151914 Hom.: 3253 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.195 AC: 29651 AN: 152032 Hom.: 3256 Cov.: 32 AF XY: 0.196 AC XY: 14530 AN XY: 74300

African (AFR) AF: 0.285 AC: 11826 AN: 41424

American (AMR) AF: 0.116 AC: 1776 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3470

East Asian (EAS) AF: 0.0929 AC: 481 AN: 5178

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2017 AN: 10570

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

European-Non Finnish (NFE) AF: 0.165 AC: 11242 AN: 67986

Other (OTH) AF: 0.173 AC: 364 AN: 2100

Alfa AF: 0.170 Hom.: 2482

Bravo AF: 0.188

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.95
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2145231; hg19: chr20-23625547;