20-7700026-G-C

Variant names:

• chr20-7700026-G-C
• rs6133466
• ENST00000839999.1:n.396+22861C>G

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.396+22861C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,012 control chromosomes in the GnomAD database, including 3,676 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 0.20 (3676 hom., cov: 33)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 2 publications found

Genes affected

ENSG00000309276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372518	XR_937230.2	n.132-779G>C		intron_variant	Intron 1 of 3
LOC105372518	XR_937231.1	n.132-779G>C		intron_variant	Intron 1 of 2
LOC105372518	XR_937232.1	n.132-779G>C		intron_variant	Intron 1 of 2
LOC105372518	XR_937233.1	n.132-779G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309276	ENST00000839999.1	n.396+22861C>G		intron_variant	Intron 3 of 4
ENSG00000309276	ENST00000840000.1	n.75+3595C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30379 AN: 151894 Hom.: 3672 Cov.: 33

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0224

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.200 AC: 30407 AN: 152012 Hom.: 3676 Cov.: 33 AF XY: 0.203 AC XY: 15084 AN XY: 74250

African (AFR) AF: 0.0813 AC: 3372 AN: 41490

American (AMR) AF: 0.214 AC: 3259 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3468

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5176

South Asian (SAS) AF: 0.208 AC: 1001 AN: 4820

European-Finnish (FIN) AF: 0.313 AC: 3294 AN: 10534

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17792 AN: 67964

Other (OTH) AF: 0.195 AC: 412 AN: 2114

Alfa AF: 0.139 Hom.: 311

Bravo AF: 0.181

Asia WGS AF: 0.122 AC: 429 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	0.99
DANN	Benign	0.51
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs6133466; hg19: chr20-7680673;