rs1693469

Variant names:

• chr4-99354745-G-A
• rs1693469

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 0.314 in 152,038 control chromosomes in the GnomAD database, including 8,904 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 0.31 (8904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 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: 0.314 AC: 47670 AN: 151918 Hom.: 8897 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.314 AC: 47694 AN: 152038 Hom.: 8904 Cov.: 32 AF XY: 0.314 AC XY: 23365 AN XY: 74314

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.0817

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.289

Alfa AF: 0.374 Hom.: 1470

Bravo AF: 0.288

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1693469; hg19: chr4-100275902;