rs3895874

Variant names:

• chr17-48970506-G-A
• rs3895874

Your query was ambiguous. Multiple possible variants found:

• chr17-48970506-G-A
• chr17-48970506-G-C
• chr17-48970506-G-T

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 0.46 in 152,044 control chromosomes in the GnomAD database, including 17,746 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 0.46 (17746 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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: 0.460 AC: 69871 AN: 151926 Hom.: 17753 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.460 AC: 69871 AN: 152044 Hom.: 17746 Cov.: 33 AF XY: 0.460 AC XY: 34214 AN XY: 74326

African (AFR) AF: 0.234 AC: 9689 AN: 41464

American (AMR) AF: 0.451 AC: 6890 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1893 AN: 3472

East Asian (EAS) AF: 0.706 AC: 3649 AN: 5168

South Asian (SAS) AF: 0.538 AC: 2595 AN: 4824

European-Finnish (FIN) AF: 0.543 AC: 5743 AN: 10578

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37672 AN: 67946

Other (OTH) AF: 0.482 AC: 1018 AN: 2112

Alfa AF: 0.515 Hom.: 45923

Bravo AF: 0.445

Asia WGS AF: 0.563 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.056
DANN	Benign	0.48
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs3895874; hg19: chr17-47047868;