rs1104548

Variant names:

• chr8-107823080-G-T
• rs1104548

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;