rs7009708

Variant names:

• chr8-22695176-G-C
• rs7009708
• ENST00000785395.1:n.287G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-22695176-G-C
• chr8-22695176-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000785395.1(ENSG00000289521):​n.287G>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 0.363 in 152,022 control chromosomes in the GnomAD database, including 10,322 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 0.36 (10322 hom., cov: 33)
• Consequence: ENSG00000289521 ENST00000785395.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 4 publications found

Genes affected

ENSG00000289521 (HGNC:):

ENSG00000253125 (HGNC:58186):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• 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 rank	MANE	Protein	UniProt
LOC105379321	XR_001745832.2	n.320G>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289521	ENST00000785395.1	n.287G>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289521	ENST00000785396.1	n.21G>C		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000289521	ENST00000785397.1	n.17G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55066 AN: 151906 Hom.: 10299 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.363 AC: 55131 AN: 152022 Hom.: 10322 Cov.: 33 AF XY: 0.363 AC XY: 26986 AN XY: 74316

African (AFR) AF: 0.298 AC: 12366 AN: 41518

American (AMR) AF: 0.371 AC: 5674 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3472

East Asian (EAS) AF: 0.433 AC: 2220 AN: 5124

South Asian (SAS) AF: 0.384 AC: 1854 AN: 4830

European-Finnish (FIN) AF: 0.415 AC: 4393 AN: 10582

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26726 AN: 67888

Other (OTH) AF: 0.363 AC: 767 AN: 2114

Alfa AF: 0.270 Hom.: 743

Bravo AF: 0.360

Asia WGS AF: 0.450 AC: 1559 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7009708; hg19: chr8-22552689; COSMIC: COSV57833476;