rs4735116

Positions:

• chr8-109209375-A-C

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 0.362 in 152,030 control chromosomes in the GnomAD database, including 10,756 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 0.36 (10756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54995 AN: 151912 Hom.: 10750 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.362 AC: 55015 AN: 152030 Hom.: 10756 Cov.: 32 AF XY: 0.368 AC XY: 27316 AN XY: 74304

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.346

Alfa AF: 0.390 Hom.: 2043

Bravo AF: 0.353

Asia WGS AF: 0.503 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4735116; hg19: chr8-110221604;