20-12668716-G-C

Variant names:

• chr20-12668716-G-C
• rs963431
• ENST00000776030.1:n.112-9565C>G

Variant summary

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

The ENST00000776030.1(ENSG00000301081):​n.112-9565C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,960 control chromosomes in the GnomAD database, including 3,008 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 0.19 (3008 hom., cov: 32)
• Consequence: ENSG00000301081 ENST00000776030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 1 publications found

Genes affected

ENSG00000301081 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776030.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301081	ENST00000776030.1		n.112-9565C>G		intron	N/A
	ENSG00000301081	ENST00000776031.1		n.135-9565C>G		intron	N/A
	ENSG00000301081	ENST00000776032.1		n.350+2012C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28085 AN: 151842 Hom.: 2994 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.185 AC: 28128 AN: 151960 Hom.: 3008 Cov.: 32 AF XY: 0.186 AC XY: 13851 AN XY: 74290

African (AFR) AF: 0.290 AC: 12026 AN: 41440

American (AMR) AF: 0.141 AC: 2153 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1597 AN: 5154

South Asian (SAS) AF: 0.204 AC: 980 AN: 4814

European-Finnish (FIN) AF: 0.121 AC: 1278 AN: 10566

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9072 AN: 67958

Other (OTH) AF: 0.195 AC: 411 AN: 2108

Alfa AF: 0.0659 Hom.: 64

Bravo AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.49
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs963431; hg19: chr20-12649363;