rs8092443

Positions:

• chr18-70475178-G-A

Variant summary

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

The ENST00000687285.1(ENSG00000288828):​n.123+10139G>A 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 0.206 in 152,138 control chromosomes in the GnomAD database, including 3,811 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 0.21 (3811 hom., cov: 32)
• Consequence: ENST00000687285.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376872	XR_935606.3	n.87+4815G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687285.1	n.123+10139G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31278 AN: 152020 Hom.: 3802 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.206 AC: 31310 AN: 152138 Hom.: 3811 Cov.: 32 AF XY: 0.202 AC XY: 15001 AN XY: 74380

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.188

Alfa AF: 0.164 Hom.: 2905

Bravo AF: 0.212

Asia WGS AF: 0.173 AC: 598 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8092443; hg19: chr18-68142414;