20-1778944-C-T

Variant names:

• chr20-1778944-C-T
• rs6080550
• ENST00000418979.2:n.335-96G>A

Variant summary

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

The ENST00000447206.2(ENSG00000286288):​n.436-96G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,166 control chromosomes in the GnomAD database, including 977 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 0.099 (977 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000286288 ENST00000447206.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 12 publications found

Genes affected

ENSG00000232528 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447206.2. 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
	LOC100289473	NR_037142.1		n.86-96G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232528	ENST00000418979.2	TSL:6	n.335-96G>A		intron	N/A
	ENSG00000286288	ENST00000447206.2	TSL:2	n.436-96G>A		intron	N/A
	ENSG00000286288	ENST00000458670.1	TSL:2	n.86-96G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15034 AN: 152048 Hom.: 973 Cov.: 32

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0989 AC: 15055 AN: 152166 Hom.: 977 Cov.: 32 AF XY: 0.0987 AC XY: 7343 AN XY: 74374

African (AFR) AF: 0.0260 AC: 1079 AN: 41520

American (AMR) AF: 0.167 AC: 2555 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1051 AN: 5172

South Asian (SAS) AF: 0.106 AC: 513 AN: 4822

European-Finnish (FIN) AF: 0.0836 AC: 883 AN: 10564

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8153 AN: 68012

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.114 Hom.: 3824

Bravo AF: 0.101

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.68
PhyloP100		0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6080550;

hg19: chr20-1759590;