rs4856162

Positions:

• chr3-103573382-G-A

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 0.423 in 151,742 control chromosomes in the GnomAD database, including 15,225 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 0.42 (15225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 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: 0.423 AC: 64114 AN: 151622 Hom.: 15172 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.423 AC: 64237 AN: 151742 Hom.: 15225 Cov.: 32 AF XY: 0.431 AC XY: 31970 AN XY: 74182

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.434

Alfa AF: 0.331 Hom.: 8892

Bravo AF: 0.438

Asia WGS AF: 0.543 AC: 1887 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4856162; hg19: chr3-103292226;