rs6107869

Variant names:

• chr20-6766908-A-G
• rs6107869
• ENST00000788333.1:n.72-103T>C

Variant summary

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

The ENST00000788333.1(ENSG00000302641):​n.72-103T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 152,306 control chromosomes in the GnomAD database, including 147 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 0.038 (147 hom., cov: 32)
• Consequence: ENSG00000302641 ENST00000788333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 5 publications found

Genes affected

ENSG00000302641 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.068 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788333.1. 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
	ENSG00000302641	ENST00000788333.1		n.72-103T>C		intron	N/A
	ENSG00000302641	ENST00000788334.1		n.89-103T>C		intron	N/A
	ENSG00000302641	ENST00000788335.1		n.199-103T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0383 AC: 5827 AN: 152188 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.0219

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0382 AC: 5823 AN: 152306 Hom.: 147 Cov.: 32 AF XY: 0.0367 AC XY: 2736 AN XY: 74478

African (AFR) AF: 0.0101 AC: 418 AN: 41574

American (AMR) AF: 0.0340 AC: 520 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3472

East Asian (EAS) AF: 0.0741 AC: 384 AN: 5180

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4828

European-Finnish (FIN) AF: 0.0277 AC: 294 AN: 10614

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3738 AN: 68018

Other (OTH) AF: 0.0436 AC: 92 AN: 2110

Alfa AF: 0.0498 Hom.: 154

Bravo AF: 0.0388

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.39
PhyloP100		0.84

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: rs6107869;

hg19: chr20-6747555;