20-46095666-A-G

Variant names:

• chr20-46095666-A-G
• rs6131010
• ENST00000758803.1:n.364-1904T>C

Variant summary

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

The ENST00000758803.1(ENSG00000298900):​n.364-1904T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,242 control chromosomes in the GnomAD database, including 47,627 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 0.79 (47627 hom., cov: 33)
• Consequence: ENSG00000298900 ENST00000758803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 18 publications found

Genes affected

ENSG00000298900 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298900	ENST00000758803.1	n.364-1904T>C		intron_variant	Intron 2 of 2
ENSG00000298900	ENST00000758804.1	n.197-1904T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119383 AN: 152124 Hom.: 47559 Cov.: 33

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.785 AC: 119512 AN: 152242 Hom.: 47627 Cov.: 33 AF XY: 0.780 AC XY: 58069 AN XY: 74440

African (AFR) AF: 0.933 AC: 38789 AN: 41556

American (AMR) AF: 0.770 AC: 11775 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2448 AN: 3472

East Asian (EAS) AF: 0.622 AC: 3222 AN: 5180

South Asian (SAS) AF: 0.756 AC: 3650 AN: 4830

European-Finnish (FIN) AF: 0.710 AC: 7526 AN: 10606

Middle Eastern (MID) AF: 0.734 AC: 213 AN: 290

European-Non Finnish (NFE) AF: 0.729 AC: 49577 AN: 67984

Other (OTH) AF: 0.766 AC: 1620 AN: 2114

Alfa AF: 0.790 Hom.: 8671

Bravo AF: 0.797

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.1
DANN	Benign	0.60
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs6131010; hg19: chr20-44724305;