rs4133274

Variant names:

• chr8-127663886-A-G
• rs4133274
• ENST00000652367.1:n.3995T>C

Variant summary

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

The ENST00000652367.1(ENSG00000286010):​n.3995T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 152,196 control chromosomes in the GnomAD database, including 795 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 (795 hom., cov: 32)
• Consequence: ENSG00000286010 ENST00000652367.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 6 publications found

Genes affected

ENSG00000286010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375754	XR_001746085.2	n.4920T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105375754	XR_001746086.2	n.3878T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105375754	XR_007061106.1	n.5012T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286010	ENST00000652367.1	n.3995T>C		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000286010	ENST00000754566.1	n.110+4828T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14090 AN: 152078 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0556

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0926 AC: 14090 AN: 152196 Hom.: 795 Cov.: 32 AF XY: 0.0968 AC XY: 7203 AN XY: 74412

African (AFR) AF: 0.103 AC: 4287 AN: 41512

American (AMR) AF: 0.0554 AC: 847 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1111 AN: 5178

South Asian (SAS) AF: 0.258 AC: 1240 AN: 4802

European-Finnish (FIN) AF: 0.106 AC: 1126 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0699 AC: 4757 AN: 68026

Other (OTH) AF: 0.0985 AC: 208 AN: 2112

Alfa AF: 0.0758 Hom.: 773

Bravo AF: 0.0863

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.85
DANN	Benign	0.60
PhyloP100		-0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4133274; hg19: chr8-128676131;