20-16590821-T-G

Variant names:

• chr20-16590821-T-G
• rs6075078
• ENST00000796242.1:n.864-205A>C

Variant summary

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

The ENST00000796242.1(ENSG00000303645):​n.864-205A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,836 control chromosomes in the GnomAD database, including 24,087 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 0.55 (24087 hom., cov: 33)
• Consequence: ENSG00000303645 ENST00000796242.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 9 publications found

Genes affected

ENSG00000303645 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796242.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303645	ENST00000796242.1		n.864-205A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83680 AN: 151718 Hom.: 24055 Cov.: 33

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.552 AC: 83765 AN: 151836 Hom.: 24087 Cov.: 33 AF XY: 0.553 AC XY: 41038 AN XY: 74232

African (AFR) AF: 0.712 AC: 29355 AN: 41256

American (AMR) AF: 0.477 AC: 7283 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3472

East Asian (EAS) AF: 0.595 AC: 3066 AN: 5154

South Asian (SAS) AF: 0.485 AC: 2338 AN: 4816

European-Finnish (FIN) AF: 0.595 AC: 6294 AN: 10576

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32447 AN: 67968

Other (OTH) AF: 0.498 AC: 1050 AN: 2110

Alfa AF: 0.493 Hom.: 73150

Bravo AF: 0.554

Asia WGS AF: 0.555 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6075078; hg19: chr20-16571466;