chr20-54182662-T-C

Variant names:

• chr20-54182662-T-C
• rs6068821
• ENST00000655028.2:n.773T>C

Variant summary

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

The ENST00000655028.2(ENSG00000286587):​n.773T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,048 control chromosomes in the GnomAD database, including 25,850 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 0.58 (25850 hom., cov: 31)
• Consequence: ENSG00000286587 ENST00000655028.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.274+28T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286587	ENST00000655028.2	n.773T>C		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000286587	ENST00000792344.1	n.279T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000286587	ENST00000792345.1	n.264T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88164 AN: 151930 Hom.: 25835 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.580 AC: 88214 AN: 152048 Hom.: 25850 Cov.: 31 AF XY: 0.579 AC XY: 43061 AN XY: 74312

African (AFR) AF: 0.566 AC: 23452 AN: 41466

American (AMR) AF: 0.594 AC: 9077 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1622 AN: 5170

South Asian (SAS) AF: 0.597 AC: 2877 AN: 4820

European-Finnish (FIN) AF: 0.583 AC: 6160 AN: 10566

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.607 AC: 41281 AN: 67982

Other (OTH) AF: 0.550 AC: 1156 AN: 2102

Alfa AF: 0.592 Hom.: 10520

Bravo AF: 0.578

Asia WGS AF: 0.488 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.39
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6068821; hg19: chr20-52799201;