rs4694178

Variant names:

• chr4-73746971-C-A
• rs4694178

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.469 in 151,790 control chromosomes in the GnomAD database, including 18,629 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 0.47 (18629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71158 AN: 151672 Hom.: 18627 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.469 AC: 71184 AN: 151790 Hom.: 18629 Cov.: 33 AF XY: 0.477 AC XY: 35375 AN XY: 74156

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.489

Alfa AF: 0.496 Hom.: 2481

Bravo AF: 0.455

Asia WGS AF: 0.596 AC: 2072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4694178; hg19: chr4-74612688;