8-2920306-C-T

Variant names:

• chr8-2920306-C-T
• rs10503186
• NR_168441.1:n.1167-80699C>T

Variant summary

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

The NR_168441.1(LOC105377785):​n.1167-80699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,156 control chromosomes in the GnomAD database, including 818 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 0.060 (818 hom., cov: 32)
• Consequence: LOC105377785 NR_168441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

LOC105377785 (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 (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.1167-80699C>T		intron_variant	Intron 6 of 11
LOC105377785	NR_168442.1	n.1697+988C>T		intron_variant	Intron 9 of 14
LOC105377785	NR_168443.1	n.1171+82542C>T		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9123 AN: 152038 Hom.: 812 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0601 AC: 9145 AN: 152156 Hom.: 818 Cov.: 32 AF XY: 0.0651 AC XY: 4839 AN XY: 74374

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0152

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0645

Alfa AF: 0.0555 Hom.: 107

Bravo AF: 0.0726

Asia WGS AF: 0.245 AC: 850 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	5.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503186; hg19: chr8-2777828;