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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929098	XR_007067503.1	n.69-241T>C		intron_variant	Intron 1 of 1
LOC101929098	XR_430278.4	n.104-241T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305741	ENST00000812739.1	n.89-241T>C		intron_variant	Intron 1 of 1
ENSG00000305741	ENST00000812740.1	n.300-241T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs6133010; hg19: chr20-3050301;