rs5030875

Positions:

• chr8-66181831-A-C

Variant summary

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

The XR_002956713.2(LOC112268029):​n.240T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 152,308 control chromosomes in the GnomAD database, including 747 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 0.077 (747 hom., cov: 33)
• Consequence: LOC112268029 XR_002956713.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.975

Genes affected

LOC112268029 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268029	XR_002956713.2	n.240T>G		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11714 AN: 152190 Hom.: 745 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0101

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0772 AC: 11751 AN: 152308 Hom.: 747 Cov.: 33 AF XY: 0.0752 AC XY: 5601 AN XY: 74470

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0389

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0101

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0465

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0701 Hom.: 82

Bravo AF: 0.0820

Asia WGS AF: 0.0270 AC: 96 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
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: rs5030875; hg19: chr8-67094066;