3-1700081-G-C

Variant names:

• chr3-1700081-G-C
• rs73001827

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 0.0973 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0251 AC: 1043 AN: 41550

American (AMR) AF: 0.0931 AC: 1423 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3470

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5176

South Asian (SAS) AF: 0.103 AC: 494 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1246 AN: 10608

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9900 AN: 68008

Other (OTH) AF: 0.0952 AC: 201 AN: 2112

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs73001827; hg19: chr3-1741765;