rs6132511

Variant names:

• chr20-22398422-A-G
• rs6132511
• ENST00000635130.1:n.688+21538T>C

Variant summary

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

The ENST00000653586.1(ENSG00000204684):​n.867+21538T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 152,098 control chromosomes in the GnomAD database, including 844 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 0.085 (844 hom., cov: 32)
• Consequence: ENSG00000204684 ENST00000653586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 5 publications found

Genes affected

ENSG00000204684 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653586.1. 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
	ENSG00000204684	ENST00000635130.1	TSL:5	n.688+21538T>C		intron	N/A
	ENSG00000204684	ENST00000653586.1		n.867+21538T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12862 AN: 151980 Hom.: 838 Cov.: 32

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.0380

Gnomad FIN AF: 0.0638

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0812

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

GnomAD4 genome AF: 0.0847 AC: 12885 AN: 152098 Hom.: 844 Cov.: 32 AF XY: 0.0856 AC XY: 6363 AN XY: 74336

African (AFR) AF: 0.0704 AC: 2923 AN: 41508

American (AMR) AF: 0.112 AC: 1706 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2073 AN: 5142

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4816

European-Finnish (FIN) AF: 0.0638 AC: 676 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4844 AN: 67988

Other (OTH) AF: 0.0818 AC: 173 AN: 2116

Alfa AF: 0.0792 Hom.: 1958

Bravo AF: 0.0921

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.34
PhyloP100		-0.61

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: rs6132511;

hg19: chr20-22379060;