rs206626

Positions:

• chr18-10321350-A-G

Variant summary

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

The ENST00000669383.1(ENSG00000287065):​n.401-1673A>G 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 0.439 in 152,028 control chromosomes in the GnomAD database, including 17,016 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 0.44 (17016 hom., cov: 32)
• Consequence: ENST00000669383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371985	XR_001753346.2	n.463+798T>C		intron_variant, non_coding_transcript_variant
LOC105371985	XR_001753345.2	n.653T>C		non_coding_transcript_exon_variant	4/4
LOC105371985	XR_007066287.1	n.552T>C		non_coding_transcript_exon_variant	3/3
LOC105371985	XR_001753344.2	n.532+798T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669383.1	n.401-1673A>G		intron_variant, non_coding_transcript_variant
	ENST00000666410.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66785 AN: 151910 Hom.: 17017 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.439 AC: 66792 AN: 152028 Hom.: 17016 Cov.: 32 AF XY: 0.442 AC XY: 32869 AN XY: 74294

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.476

Alfa AF: 0.499 Hom.: 3407

Bravo AF: 0.433

Asia WGS AF: 0.532 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs206626; hg19: chr18-10321347; COSMIC: COSV73862170;