chr20-54178708-T-G

Variant names:

• chr20-54178708-T-G
• rs2426496
• ENST00000655028.2:n.666+220T>G

Variant summary

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

The ENST00000655028.2(ENSG00000286587):​n.666+220T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,950 control chromosomes in the GnomAD database, including 32,626 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 0.65 (32626 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000655028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 8 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.195+220T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286587	ENST00000655028.2	n.666+220T>G		intron_variant	Intron 4 of 4
ENSG00000286587	ENST00000792273.1	n.288+10137T>G		intron_variant	Intron 3 of 3
ENSG00000286587	ENST00000792274.1	n.375+220T>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99027 AN: 151832 Hom.: 32609 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.652 AC: 99086 AN: 151950 Hom.: 32626 Cov.: 32 AF XY: 0.652 AC XY: 48439 AN XY: 74258

African (AFR) AF: 0.562 AC: 23248 AN: 41390

American (AMR) AF: 0.710 AC: 10849 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1950 AN: 3470

East Asian (EAS) AF: 0.640 AC: 3306 AN: 5166

South Asian (SAS) AF: 0.641 AC: 3085 AN: 4812

European-Finnish (FIN) AF: 0.698 AC: 7375 AN: 10560

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47127 AN: 67960

Other (OTH) AF: 0.632 AC: 1333 AN: 2108

Alfa AF: 0.661 Hom.: 4835

Bravo AF: 0.650

Asia WGS AF: 0.620 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.60
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2426496; hg19: chr20-52795247;