rs1895858

Variant names:

• chr3-139930821-T-C
• rs1895858

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 0.248 in 152,214 control chromosomes in the GnomAD database, including 5,082 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 0.25 (5082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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: 0.249 AC: 37820 AN: 152096 Hom.: 5083 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.248 AC: 37813 AN: 152214 Hom.: 5082 Cov.: 32 AF XY: 0.243 AC XY: 18117 AN XY: 74416

African (AFR) AF: 0.174 AC: 7239 AN: 41534

American (AMR) AF: 0.197 AC: 3011 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1122 AN: 5186

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4820

European-Finnish (FIN) AF: 0.202 AC: 2138 AN: 10592

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 21004 AN: 68004

Other (OTH) AF: 0.234 AC: 494 AN: 2114

Alfa AF: 0.292 Hom.: 3399

Bravo AF: 0.243

Asia WGS AF: 0.234 AC: 812 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.6
DANN	Benign	0.62
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1895858; hg19: chr3-139649663;