rs789063

Positions:

• chr18-1006469-A-G
• chr18-1006469-A-T

Variant summary

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

The XR_001753317.1(LOC107985165):​n.151-43551A>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 0.344 in 152,142 control chromosomes in the GnomAD database, including 13,125 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 0.34 (13125 hom., cov: 32)
• Consequence: LOC107985165 XR_001753317.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

LOC107985165 (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 (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985165	XR_001753317.1	n.151-43551A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000577719.5	n.307+29574A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000579835.5	n.199+29574A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000580781.5	n.306+29574A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52260 AN: 152024 Hom.: 13094 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.344 AC: 52347 AN: 152142 Hom.: 13125 Cov.: 32 AF XY: 0.339 AC XY: 25242 AN XY: 74394

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.325

Alfa AF: 0.223 Hom.: 8659

Bravo AF: 0.366

Asia WGS AF: 0.350 AC: 1218 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	7.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs789063; hg19: chr18-1006470;