6-28865730-C-T

Variant names:

• chr6-28865730-C-T
• rs9257280
• ENST00000773451.1:n.193G>A

Variant summary

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

The ENST00000773451.1(ENSG00000300690):​n.193G>A 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 0.259 in 152,082 control chromosomes in the GnomAD database, including 5,410 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 0.26 (5410 hom., cov: 33)
• Consequence: ENSG00000300690 ENST00000773451.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 9 publications found

Genes affected

ENSG00000300690 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300690	ENST00000773451.1	n.193G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39354 AN: 151964 Hom.: 5410 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.259 AC: 39362 AN: 152082 Hom.: 5410 Cov.: 33 AF XY: 0.264 AC XY: 19629 AN XY: 74350

African (AFR) AF: 0.249 AC: 10339 AN: 41446

American (AMR) AF: 0.316 AC: 4827 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1102 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2625 AN: 5178

South Asian (SAS) AF: 0.348 AC: 1678 AN: 4822

European-Finnish (FIN) AF: 0.209 AC: 2207 AN: 10568

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15533 AN: 67994

Other (OTH) AF: 0.266 AC: 562 AN: 2112

Alfa AF: 0.245 Hom.: 4601

Bravo AF: 0.266

Asia WGS AF: 0.377 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.0
DANN	Benign	0.52
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs9257280; hg19: chr6-28833507;