rs5030876

Positions:

• chr8-66180813-A-G

Variant summary

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

The XR_002956713.2(LOC112268029):​n.249-853T>C 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 152,142 control chromosomes in the GnomAD database, including 8,453 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 (8453 hom., cov: 32)
• Consequence: LOC112268029 XR_002956713.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

LOC112268029 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268029	XR_002956713.2	n.249-853T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35575 AN: 152024 Hom.: 8420 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.234 AC: 35663 AN: 152142 Hom.: 8453 Cov.: 32 AF XY: 0.228 AC XY: 16950 AN XY: 74400

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0962

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.189

Alfa AF: 0.189 Hom.: 702

Bravo AF: 0.251

Asia WGS AF: 0.0620 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5030876; hg19: chr8-67093048;