rs34418712

Positions:

• chr4-189467222-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.00196

Gnomad4 AMR AF: 0.00296

Gnomad4 ASJ AF: 0.00954

Gnomad4 EAS AF: 0.000829

Gnomad4 SAS AF: 0.00197

Gnomad4 FIN AF: 0.00199

Gnomad4 NFE AF: 0.00505

Gnomad4 OTH AF: 0.00165

Alfa AF: 0.135 Hom.: 122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34418712; hg19: chr4-190388376;