rs10098823

Positions:

• chr8-66183392-C-A

Variant summary

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

The XR_002956713.2(LOC112268029):​n.89-401G>T 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 0.156 in 152,036 control chromosomes in the GnomAD database, including 4,094 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 0.16 (4094 hom., cov: 32)
• Consequence: LOC112268029 XR_002956713.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

Genes affected

LOC112268029 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268029	XR_002956713.2	n.89-401G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23733 AN: 151918 Hom.: 4083 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.156 AC: 23781 AN: 152036 Hom.: 4094 Cov.: 32 AF XY: 0.152 AC XY: 11280 AN XY: 74316

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.0838

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0492

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0959 Hom.: 814

Bravo AF: 0.168

Asia WGS AF: 0.0340 AC: 118 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10098823; hg19: chr8-67095627;