rs5030877

Positions:

• chr8-66181991-G-C

Variant summary

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

The XR_002956713.2(LOC112268029):​n.190-110C>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 0.234 in 152,134 control chromosomes in the GnomAD database, including 8,402 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 0.23 (8402 hom., cov: 32)
• Consequence: LOC112268029 XR_002956713.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71

Genes affected

LOC112268029 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268029	XR_002956713.2	n.190-110C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35504 AN: 152016 Hom.: 8370 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0734

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.234 AC: 35589 AN: 152134 Hom.: 8402 Cov.: 32 AF XY: 0.228 AC XY: 16929 AN XY: 74384

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0734

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0962

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.188

Alfa AF: 0.189 Hom.: 700

Bravo AF: 0.250

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.033
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5030877; hg19: chr8-67094226;