rs28361085

Variant names:

• chr6-33130747-T-C
• rs28361085
• ENST00000783029.1:n.1083A>G

Variant summary

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

The ENST00000783029.1(ENSG00000301948):​n.1083A>G 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 0.0893 in 152,286 control chromosomes in the GnomAD database, including 768 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 0.089 (768 hom., cov: 32)
• Consequence: ENSG00000301948 ENST00000783029.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 1 publications found

Genes affected

ENSG00000301948 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375021	NR_190905.1	n.991A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301948	ENST00000783029.1	n.1083A>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000301948	ENST00000783030.1	n.1011A>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000301948	ENST00000783031.1	n.1210A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0894 AC: 13597 AN: 152168 Hom.: 766 Cov.: 32

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.0893 AC: 13604 AN: 152286 Hom.: 768 Cov.: 32 AF XY: 0.0926 AC XY: 6895 AN XY: 74456

African (AFR) AF: 0.0559 AC: 2321 AN: 41550

American (AMR) AF: 0.0738 AC: 1130 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.0501 AC: 260 AN: 5194

South Asian (SAS) AF: 0.250 AC: 1205 AN: 4824

European-Finnish (FIN) AF: 0.0741 AC: 785 AN: 10600

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6974 AN: 68016

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.0984 Hom.: 233

Bravo AF: 0.0837

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.57
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs28361085; hg19: chr6-33098524;