rs9486902

Variant names:

• chr6-108556849-C-T
• rs9486902
• ENST00000784396.1:n.702G>A

Variant summary

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

The ENST00000784396.1(ENSG00000287044):​n.702G>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 0.177 in 152,138 control chromosomes in the GnomAD database, including 2,609 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 0.18 (2609 hom., cov: 32)
• Consequence: ENSG00000287044 ENST00000784396.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 24 publications found

Genes affected

ENSG00000287044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901372	XR_007059700.1	n.343+1315G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287044	ENST00000784396.1	n.702G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287044	ENST00000659932.2	n.136+1315G>A		intron_variant	Intron 1 of 3
ENSG00000287044	ENST00000784390.1	n.119+1315G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26974 AN: 152020 Hom.: 2606 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.177 AC: 26992 AN: 152138 Hom.: 2609 Cov.: 32 AF XY: 0.172 AC XY: 12812 AN XY: 74380

African (AFR) AF: 0.234 AC: 9716 AN: 41482

American (AMR) AF: 0.217 AC: 3314 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0861 AC: 299 AN: 3472

East Asian (EAS) AF: 0.0579 AC: 300 AN: 5180

South Asian (SAS) AF: 0.121 AC: 585 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1187 AN: 10578

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11012 AN: 67996

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.171 Hom.: 8845

Bravo AF: 0.190

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9486902; hg19: chr6-108878052; COSMIC: COSV59627004;