rs1104548

Positions:

• chr8-107823080-G-T

Variant summary

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

The variant allele was found at a frequency of 0.126 in 152,044 control chromosomes in the GnomAD database, including 3,203 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 0.13 (3203 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.107823080G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19143 AN: 151928 Hom.: 3183 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00875

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.126 AC: 19193 AN: 152044 Hom.: 3203 Cov.: 32 AF XY: 0.125 AC XY: 9290 AN XY: 74344

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0259

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.0634

Gnomad4 FIN AF: 0.0384

Gnomad4 NFE AF: 0.00875

Gnomad4 OTH AF: 0.0905

Alfa AF: 0.0755 Hom.: 235

Bravo AF: 0.138

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.61
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1104548; hg19: chr8-108835308;