20-7675563-G-C

Variant names:

• chr20-7675563-G-C
• rs2143197
• ENST00000839999.1:n.397-6564C>G

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.397-6564C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 151,668 control chromosomes in the GnomAD database, including 59,189 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 0.88 (59189 hom., cov: 28)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• 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 (EAS) allele frequency at 95% confidence interval = 0.977 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.397-6564C>G		intron	N/A
	ENSG00000309276	ENST00000840000.1		n.76-6564C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.882 AC: 133695 AN: 151550 Hom.: 59136 Cov.: 28

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.846

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.882 AC: 133805 AN: 151668 Hom.: 59189 Cov.: 28 AF XY: 0.884 AC XY: 65540 AN XY: 74108

African (AFR) AF: 0.903 AC: 37401 AN: 41402

American (AMR) AF: 0.910 AC: 13888 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2865 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5120 AN: 5122

South Asian (SAS) AF: 0.948 AC: 4539 AN: 4788

European-Finnish (FIN) AF: 0.839 AC: 8763 AN: 10442

Middle Eastern (MID) AF: 0.845 AC: 245 AN: 290

European-Non Finnish (NFE) AF: 0.860 AC: 58358 AN: 67892

Other (OTH) AF: 0.876 AC: 1838 AN: 2098

Alfa AF: 0.818 Hom.: 2450

Bravo AF: 0.889

Asia WGS AF: 0.969 AC: 3329 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.56
PhyloP100		-0.0090

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: rs2143197;

hg19: chr20-7656210;