20-3069074-G-C

Variant names:

• chr20-3069074-G-C
• rs4813625
• ENST00000812739.1:n.429C>G

Variant summary

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

The ENST00000812739.1(ENSG00000305741):​n.429C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,150 control chromosomes in the GnomAD database, including 17,982 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 (17982 hom., cov: 33)
• Consequence: ENSG00000305741 ENST00000812739.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 24 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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929098	XR_007067503.1	n.409C>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC101929098	XR_430278.4	n.444C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305741	ENST00000812739.1	n.429C>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000305741	ENST00000812740.1	n.640C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73686 AN: 152032 Hom.: 17960 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.485 AC: 73759 AN: 152150 Hom.: 17982 Cov.: 33 AF XY: 0.485 AC XY: 36071 AN XY: 74376

African (AFR) AF: 0.504 AC: 20925 AN: 41516

American (AMR) AF: 0.498 AC: 7610 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1684 AN: 3472

East Asian (EAS) AF: 0.462 AC: 2386 AN: 5170

South Asian (SAS) AF: 0.526 AC: 2541 AN: 4828

European-Finnish (FIN) AF: 0.469 AC: 4954 AN: 10570

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32311 AN: 67988

Other (OTH) AF: 0.446 AC: 943 AN: 2112

Alfa AF: 0.349 Hom.: 914

Bravo AF: 0.487

Asia WGS AF: 0.560 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.63
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4813625; hg19: chr20-3049720;