20-7699400-C-T

Variant names:

• chr20-7699400-C-T
• rs6133460
• ENST00000839999.1:n.396+23487G>A

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.396+23487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 149,500 control chromosomes in the GnomAD database, including 3,682 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 (3682 hom., cov: 33)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839999.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309276	ENST00000839999.1		n.396+23487G>A		intron	N/A
	ENSG00000309276	ENST00000840000.1		n.75+4221G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30395 AN: 149378 Hom.: 3678 Cov.: 33

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.203 AC: 30423 AN: 149500 Hom.: 3682 Cov.: 33 AF XY: 0.207 AC XY: 15113 AN XY: 73148

African (AFR) AF: 0.0837 AC: 3387 AN: 40446

American (AMR) AF: 0.219 AC: 3261 AN: 14916

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 766 AN: 3410

East Asian (EAS) AF: 0.0232 AC: 119 AN: 5134

South Asian (SAS) AF: 0.212 AC: 1000 AN: 4728

European-Finnish (FIN) AF: 0.316 AC: 3314 AN: 10472

Middle Eastern (MID) AF: 0.215 AC: 61 AN: 284

European-Non Finnish (NFE) AF: 0.265 AC: 17773 AN: 67148

Other (OTH) AF: 0.199 AC: 411 AN: 2062

Alfa AF: 0.232 Hom.: 7377

Bravo AF: 0.181

Asia WGS AF: 0.122 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.49
PhyloP100		-0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6133460;

hg19: chr20-7680047;