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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372541	XR_937285.3	n.964-205A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303645	ENST00000796242.1	n.864-205A>C		intron_variant	Intron 1 of 1

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 v4.3

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;