20-7775380-G-A

Variant names:

• chr20-7775380-G-A
• rs2092380
• ENST00000839999.1:n.282+27445C>T

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.282+27445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,030 control chromosomes in the GnomAD database, including 1,050 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 0.11 (1050 hom., cov: 32)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 7 publications found

Genes affected

ENSG00000309276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839999.1. 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
	ENSG00000309276	ENST00000839999.1		n.282+27445C>T		intron	N/A
	ENSG00000309276	ENST00000840001.1		n.320-4086C>T		intron	N/A
	ENSG00000309276	ENST00000840002.1		n.86-4086C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16386 AN: 151912 Hom.: 1044 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.108 AC: 16400 AN: 152030 Hom.: 1050 Cov.: 32 AF XY: 0.110 AC XY: 8142 AN XY: 74296

African (AFR) AF: 0.101 AC: 4190 AN: 41442

American (AMR) AF: 0.151 AC: 2310 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3468

East Asian (EAS) AF: 0.147 AC: 761 AN: 5174

South Asian (SAS) AF: 0.307 AC: 1476 AN: 4810

European-Finnish (FIN) AF: 0.0615 AC: 650 AN: 10566

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0895 AC: 6086 AN: 68000

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.102 Hom.: 1817

Bravo AF: 0.113

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.55
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2092380; hg19: chr20-7756027;