3-194857561-G-C

Variant names:

• chr3-194857561-G-C
• rs225

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 0.48 in 151,970 control chromosomes in the GnomAD database, including 18,190 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 0.48 (18190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 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: 0.480 AC: 72817 AN: 151852 Hom.: 18149 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.480 AC: 72903 AN: 151970 Hom.: 18190 Cov.: 32 AF XY: 0.477 AC XY: 35455 AN XY: 74282

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.447

Alfa AF: 0.451 Hom.: 1932

Bravo AF: 0.494

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225; hg19: chr3-194578290;