rs8096007

Variant names:

• chr18-2209867-G-A
• rs8096007
• ENST00000579097.1:n.88+29926C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-2209867-G-A
• chr18-2209867-G-T

Variant summary

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

The ENST00000579097.1(ENSG00000263745):​n.88+29926C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,878 control chromosomes in the GnomAD database, including 9,432 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 0.33 (9432 hom., cov: 32)
• Consequence: ENSG00000263745 ENST00000579097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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
ENSG00000263745	ENST00000579097.1	n.88+29926C>T		intron_variant	Intron 1 of 3	2
ENSG00000263745	ENST00000584867.1	n.196+29926C>T		intron_variant	Intron 2 of 5	2
ENSG00000263745	ENST00000639316.2	n.441+29926C>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49275 AN: 151760 Hom.: 9402 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.325 AC: 49363 AN: 151878 Hom.: 9432 Cov.: 32 AF XY: 0.331 AC XY: 24574 AN XY: 74188

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.293

Alfa AF: 0.280 Hom.: 2148

Bravo AF: 0.344

Asia WGS AF: 0.543 AC: 1878 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8096007; hg19: chr18-2209867;