rs4695146

Variant names:

• chr4-46168944-A-G
• rs4695146

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 0.434 in 151,962 control chromosomes in the GnomAD database, including 14,713 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 0.43 (14713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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: 0.434 AC: 65854 AN: 151844 Hom.: 14702 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.434 AC: 65909 AN: 151962 Hom.: 14713 Cov.: 32 AF XY: 0.430 AC XY: 31897 AN XY: 74250

African (AFR) AF: 0.381 AC: 15792 AN: 41444

American (AMR) AF: 0.413 AC: 6294 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1595 AN: 5178

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4814

European-Finnish (FIN) AF: 0.461 AC: 4858 AN: 10536

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33210 AN: 67952

Other (OTH) AF: 0.426 AC: 898 AN: 2110

Alfa AF: 0.441 Hom.: 2626

Bravo AF: 0.429

Asia WGS AF: 0.304 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs4695146; hg19: chr4-46170961;