4-110806007-C-G

Variant names:

• chr4-110806007-C-G
• rs3855819

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 0.237 in 151,634 control chromosomes in the GnomAD database, including 4,953 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 0.24 (4953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 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: 0.237 AC: 35884 AN: 151514 Hom.: 4940 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.237 AC: 35926 AN: 151634 Hom.: 4953 Cov.: 32 AF XY: 0.234 AC XY: 17291 AN XY: 74040

African (AFR) AF: 0.398 AC: 16466 AN: 41360

American (AMR) AF: 0.219 AC: 3321 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 598 AN: 3466

East Asian (EAS) AF: 0.179 AC: 921 AN: 5154

South Asian (SAS) AF: 0.244 AC: 1174 AN: 4816

European-Finnish (FIN) AF: 0.154 AC: 1622 AN: 10552

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11044 AN: 67818

Other (OTH) AF: 0.224 AC: 471 AN: 2106

Alfa AF: 0.0761 Hom.: 88

Bravo AF: 0.252

Asia WGS AF: 0.230 AC: 798 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.48
DANN	Benign	0.54
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs3855819; hg19: chr4-111727163;