chr20-48300766-C-T

Variant names:

• chr20-48300766-C-T
• rs969127
• ENST00000806334.1:n.281-9199G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000806334.1(ENSG00000304799):​n.281-9199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 151,620 control chromosomes in the GnomAD database, including 594 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 0.060 (594 hom., cov: 32)
• Consequence: ENSG00000304799 ENST00000806334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 0 publications found

Genes affected

ENSG00000304799 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806334.1. 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
	ENSG00000304799	ENST00000806334.1		n.281-9199G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0597 AC: 9049 AN: 151502 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.00636

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00930

Gnomad OTH AF: 0.0563

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

GnomAD4 genome AF: 0.0599 AC: 9081 AN: 151620 Hom.: 594 Cov.: 32 AF XY: 0.0614 AC XY: 4549 AN XY: 74078

African (AFR) AF: 0.137 AC: 5653 AN: 41286

American (AMR) AF: 0.0612 AC: 929 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.00636 AC: 22 AN: 3460

East Asian (EAS) AF: 0.235 AC: 1208 AN: 5138

South Asian (SAS) AF: 0.0684 AC: 325 AN: 4752

European-Finnish (FIN) AF: 0.0174 AC: 184 AN: 10554

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00930 AC: 632 AN: 67936

Other (OTH) AF: 0.0571 AC: 120 AN: 2102

Alfa AF: 0.0353 Hom.: 34

Bravo AF: 0.0670

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	17
DANN	Benign	0.78
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs969127; hg19: chr20-46929509;