3-1700081-G-C

Position:

• chr3-1700081-G-C

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 0.0973 in 152,236 control chromosomes in the GnomAD database, including 913 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 0.097 (913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

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: 0.0974 AC: 14809 AN: 152118 Hom.: 914 Cov.: 33

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0973 AC: 14808 AN: 152236 Hom.: 913 Cov.: 33 AF XY: 0.0962 AC XY: 7162 AN XY: 74444

Gnomad4 AFR AF: 0.0251

Gnomad4 AMR AF: 0.0931

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.0952

Alfa AF: 0.111 Hom.: 153

Bravo AF: 0.0909

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73001827; hg19: chr3-1741765;