rs1698041

Variant names:

• chr3-117480904-T-C
• rs1698041

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.404 in 152,096 control chromosomes in the GnomAD database, including 14,915 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 0.40 (14915 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 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: 0.405 AC: 61524 AN: 151978 Hom.: 14921 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.404 AC: 61500 AN: 152096 Hom.: 14915 Cov.: 32 AF XY: 0.399 AC XY: 29626 AN XY: 74324

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.414

Alfa AF: 0.431 Hom.: 3146

Bravo AF: 0.378

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1698041; hg19: chr3-117199751;