rs6133010

Variant names:

• chr20-3069655-A-G
• rs6133010
• ENST00000812739.1:n.89-241T>C

Variant summary

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

The ENST00000812739.1(ENSG00000305741):​n.89-241T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 152,214 control chromosomes in the GnomAD database, including 718 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 0.093 (718 hom., cov: 33)
• Consequence: ENSG00000305741 ENST00000812739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 13 publications found

Genes affected

ENSG00000305741 (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 (SAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812739.1. 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
	ENSG00000305741	ENST00000812739.1		n.89-241T>C		intron	N/A
	ENSG00000305741	ENST00000812740.1		n.300-241T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14192 AN: 152096 Hom.: 717 Cov.: 33

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0901

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0933 AC: 14197 AN: 152214 Hom.: 718 Cov.: 33 AF XY: 0.0936 AC XY: 6968 AN XY: 74408

African (AFR) AF: 0.0543 AC: 2256 AN: 41546

American (AMR) AF: 0.0900 AC: 1375 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.0874 AC: 452 AN: 5174

South Asian (SAS) AF: 0.112 AC: 540 AN: 4818

European-Finnish (FIN) AF: 0.132 AC: 1396 AN: 10600

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7419 AN: 68008

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0936 Hom.: 92

Bravo AF: 0.0885

Asia WGS AF: 0.102 AC: 357 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	1.5
DANN	Benign	0.49
PhyloP100		-0.51

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: rs6133010;

hg19: chr20-3050301;