chr8-109209375-A-C

Variant names:

• chr8-109209375-A-C
• rs4735116

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.220 AC: 9139 AN: 41486

American (AMR) AF: 0.451 AC: 6883 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2437 AN: 5156

South Asian (SAS) AF: 0.497 AC: 2397 AN: 4824

European-Finnish (FIN) AF: 0.453 AC: 4783 AN: 10556

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27171 AN: 67964

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.385 Hom.: 2057

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4735116; hg19: chr8-110221604;