rs3853445

Variant names:

• chr4-110840331-T-C
• rs3853445

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 0.228 in 152,140 control chromosomes in the GnomAD database, including 4,526 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 0.23 (4526 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 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: 0.228 AC: 34619 AN: 152022 Hom.: 4522 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.228 AC: 34633 AN: 152140 Hom.: 4526 Cov.: 32 AF XY: 0.232 AC XY: 17254 AN XY: 74370

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.234

Alfa AF: 0.263 Hom.: 11562

Bravo AF: 0.226

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3853445; hg19: chr4-111761487;