rs9454847

Variant names:

• chr6-69625400-A-G
• rs9454847
• ENST00000805732.1:n.78T>C

Variant summary

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

The ENST00000805732.1(ENSG00000304708):​n.78T>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 0.0498 in 152,312 control chromosomes in the GnomAD database, including 485 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 0.050 (485 hom., cov: 32)
• Consequence: ENSG00000304708 ENST00000805732.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 1 publications found

Genes affected

ENSG00000304708 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805732.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304708	ENST00000805732.1		n.78T>C		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7566 AN: 152194 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.00518

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00961

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0498 AC: 7587 AN: 152312 Hom.: 485 Cov.: 32 AF XY: 0.0501 AC XY: 3730 AN XY: 74482

African (AFR) AF: 0.144 AC: 5977 AN: 41550

American (AMR) AF: 0.0261 AC: 400 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3470

East Asian (EAS) AF: 0.0322 AC: 167 AN: 5190

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4828

European-Finnish (FIN) AF: 0.00518 AC: 55 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00961 AC: 654 AN: 68034

Other (OTH) AF: 0.0303 AC: 64 AN: 2114

Alfa AF: 0.0300 Hom.: 42

Bravo AF: 0.0553

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.42
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs9454847; hg19: chr6-70335292;