rs4356827

Variant names:

• chr3-117459897-C-A
• rs4356827

Your query was ambiguous. Multiple possible variants found:

• chr3-117459897-C-A
• chr3-117459897-C-T

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 0.555 in 151,946 control chromosomes in the GnomAD database, including 23,795 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 0.56 (23795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.944

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 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: 0.555 AC: 84333 AN: 151828 Hom.: 23801 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.555 AC: 84348 AN: 151946 Hom.: 23795 Cov.: 32 AF XY: 0.552 AC XY: 40994 AN XY: 74258

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.580

Alfa AF: 0.544 Hom.: 4016

Bravo AF: 0.546

Asia WGS AF: 0.559 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4356827; hg19: chr3-117178744;