3-194857561-G-C

Variant names:

• chr3-194857561-G-C
• rs225

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.603 AC: 24960 AN: 41426

American (AMR) AF: 0.572 AC: 8746 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1249 AN: 3464

East Asian (EAS) AF: 0.325 AC: 1678 AN: 5166

South Asian (SAS) AF: 0.446 AC: 2143 AN: 4808

European-Finnish (FIN) AF: 0.415 AC: 4386 AN: 10558

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28209 AN: 67952

Other (OTH) AF: 0.447 AC: 942 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs225; hg19: chr3-194578290;