20-3070645-A-G

Variant names:

• chr20-3070645-A-G
• rs4813626
• ENST00000812739.1:n.89-1231T>C

Variant summary

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

The ENST00000812739.1(ENSG00000305741):​n.89-1231T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,610 control chromosomes in the GnomAD database, including 17,668 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 0.48 (17668 hom., cov: 30)
• Consequence: ENSG00000305741 ENST00000812739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 5 publications found

Genes affected

ENSG00000305741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929098	XR_007067503.1	n.68+911T>C		intron_variant	Intron 1 of 1
LOC101929098	XR_430278.4	n.104-1231T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305741	ENST00000812739.1	n.89-1231T>C		intron_variant	Intron 1 of 1
ENSG00000305741	ENST00000812740.1	n.299+911T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72374 AN: 151492 Hom.: 17644 Cov.: 30

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.478 AC: 72458 AN: 151610 Hom.: 17668 Cov.: 30 AF XY: 0.479 AC XY: 35453 AN XY: 74090

African (AFR) AF: 0.551 AC: 22785 AN: 41328

American (AMR) AF: 0.486 AC: 7400 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2282 AN: 5116

South Asian (SAS) AF: 0.529 AC: 2543 AN: 4806

European-Finnish (FIN) AF: 0.448 AC: 4706 AN: 10512

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.440 AC: 29841 AN: 67858

Other (OTH) AF: 0.420 AC: 885 AN: 2108

Alfa AF: 0.449 Hom.: 1915

Bravo AF: 0.483

Asia WGS AF: 0.551 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.86
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs4813626; hg19: chr20-3051291;