3-154465773-G-C

Variant names:

• chr3-154465773-G-C
• rs1356122

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 0.167 in 152,016 control chromosomes in the GnomAD database, including 2,148 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 0.17 (2148 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 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: 0.167 AC: 25354 AN: 151898 Hom.: 2143 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.167 AC: 25379 AN: 152016 Hom.: 2148 Cov.: 32 AF XY: 0.166 AC XY: 12326 AN XY: 74338

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.187

Alfa AF: 0.0812 Hom.: 108

Bravo AF: 0.169

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1356122; hg19: chr3-154183562;