chr3-122670146-T-C

Variant names:

• chr3-122670146-T-C
• rs790123

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 0.452 in 151,724 control chromosomes in the GnomAD database, including 16,157 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 0.45 (16157 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.452 AC: 68545 AN: 151602 Hom.: 16111 Cov.: 30

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.452 AC: 68652 AN: 151724 Hom.: 16157 Cov.: 30 AF XY: 0.461 AC XY: 34194 AN XY: 74126

African (AFR) AF: 0.565 AC: 23377 AN: 41348

American (AMR) AF: 0.477 AC: 7247 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1299 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2766 AN: 5150

South Asian (SAS) AF: 0.496 AC: 2393 AN: 4820

European-Finnish (FIN) AF: 0.529 AC: 5551 AN: 10498

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24724 AN: 67942

Other (OTH) AF: 0.446 AC: 935 AN: 2098

Alfa AF: 0.390 Hom.: 38425

Bravo AF: 0.454

Asia WGS AF: 0.518 AC: 1801 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	0.49
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs790123; hg19: chr3-122388993;