rs8096007

Positions:

• 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 ENST00000639316.2(ENSG00000263745):​n.441+29926C>T 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 0.325 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: ENST00000639316.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000639316.2	n.441+29926C>T		intron_variant, non_coding_transcript_variant		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;