rs2174304

Variant names:

• chr4-146586311-G-A
• rs2174304

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 0.122 in 152,018 control chromosomes in the GnomAD database, including 1,244 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 0.12 (1244 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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: 0.122 AC: 18560 AN: 151900 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.122 AC: 18576 AN: 152018 Hom.: 1244 Cov.: 32 AF XY: 0.118 AC XY: 8779 AN XY: 74294

African (AFR) AF: 0.152 AC: 6318 AN: 41442

American (AMR) AF: 0.0903 AC: 1380 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3468

East Asian (EAS) AF: 0.0296 AC: 153 AN: 5174

South Asian (SAS) AF: 0.103 AC: 497 AN: 4814

European-Finnish (FIN) AF: 0.102 AC: 1075 AN: 10548

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8219 AN: 67976

Other (OTH) AF: 0.121 AC: 256 AN: 2114

Alfa AF: 0.117 Hom.: 183

Bravo AF: 0.122

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.51
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2174304; hg19: chr4-147507463;