rs9295895

chr6-30470449-T-Cchr6-30470449-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685067.1(ENSG00000288805):n.386-5476A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,156 control chromosomes in the GnomAD database, including 4,488 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 0.24 (4488 hom., cov: 32)
• Consequence: ENST00000685067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685067.1	n.386-5476A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36149 AN: 152036 Hom.: 4487 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.238 AC: 36162 AN: 152156 Hom.: 4488 Cov.: 32 AF XY: 0.243 AC XY: 18088 AN XY: 74412

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.221

Alfa AF: 0.229 Hom.: 5245

Bravo AF: 0.231

Asia WGS AF: 0.317 AC: 1100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295895; hg19: chr6-30438226;