chr20-43657322-C-G

Variant names:

• chr20-43657322-C-G
• rs412396
• ENST00000770667.1:n.182G>C

Variant summary

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

The ENST00000770667.1(ENSG00000300296):​n.182G>C 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 0.774 in 151,998 control chromosomes in the GnomAD database, including 45,753 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 0.77 (45753 hom., cov: 30)
• Consequence: ENSG00000300296 ENST00000770667.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 4 publications found

Genes affected

ENSG00000300296 (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 (NFE) allele frequency at 95% confidence interval = 0.798 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
ENSG00000300296	ENST00000770667.1	n.182G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117491 AN: 151880 Hom.: 45728 Cov.: 30

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.774 AC: 117571 AN: 151998 Hom.: 45753 Cov.: 30 AF XY: 0.777 AC XY: 57725 AN XY: 74262

African (AFR) AF: 0.692 AC: 28694 AN: 41436

American (AMR) AF: 0.795 AC: 12131 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2846 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4105 AN: 5148

South Asian (SAS) AF: 0.781 AC: 3764 AN: 4820

European-Finnish (FIN) AF: 0.832 AC: 8795 AN: 10572

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54632 AN: 67972

Other (OTH) AF: 0.771 AC: 1626 AN: 2110

Alfa AF: 0.788 Hom.: 5876

Bravo AF: 0.764

Asia WGS AF: 0.769 AC: 2673 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	1.2
DANN	Benign	0.66
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs412396; hg19: chr20-42285962;