rs10086780

Positions:

• chr8-108966300-T-C

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.265-47654A>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 0.399 in 151,940 control chromosomes in the GnomAD database, including 13,645 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 0.40 (13645 hom., cov: 32)
• Consequence: ENST00000522244.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

(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 = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984017	XR_001745734.1	n.78-2242A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522244.1	n.265-47654A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60486 AN: 151820 Hom.: 13602 Cov.: 32

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.399 AC: 60598 AN: 151940 Hom.: 13645 Cov.: 32 AF XY: 0.406 AC XY: 30132 AN XY: 74248

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.379

Alfa AF: 0.303 Hom.: 15773

Bravo AF: 0.416

Asia WGS AF: 0.389 AC: 1353 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	1.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10086780; hg19: chr8-109978529;