rs34418712

Variant names:

• chr4-189467222-G-T
• rs34418712

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.0035 in 91,732 control chromosomes in the GnomAD database, including 5 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 0.0035 (5 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BS2: High Homozygotes in GnomAd4 at 5 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.00350 AC: 321 AN: 91668 Hom.: 5 Cov.: 23

Gnomad AFR AF: 0.00197

Gnomad AMI AF: 0.00643

Gnomad AMR AF: 0.00297

Gnomad ASJ AF: 0.00954

Gnomad EAS AF: 0.000826

Gnomad SAS AF: 0.00197

Gnomad FIN AF: 0.00199

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00505

Gnomad OTH AF: 0.00167

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

GnomAD4 genome AF: 0.00350 AC: 321 AN: 91732 Hom.: 5 Cov.: 23 AF XY: 0.00349 AC XY: 159 AN XY: 45558

African (AFR) AF: 0.00196 AC: 52 AN: 26514

American (AMR) AF: 0.00296 AC: 28 AN: 9454

Ashkenazi Jewish (ASJ) AF: 0.00954 AC: 17 AN: 1782

East Asian (EAS) AF: 0.000829 AC: 3 AN: 3620

South Asian (SAS) AF: 0.00197 AC: 6 AN: 3040

European-Finnish (FIN) AF: 0.00199 AC: 13 AN: 6526

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 116

European-Non Finnish (NFE) AF: 0.00505 AC: 196 AN: 38846

Other (OTH) AF: 0.00165 AC: 2 AN: 1212

Alfa AF: 0.135 Hom.: 122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	4.7
DANN	Benign	0.20
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs34418712; hg19: chr4-190388376;