rs4666734

Positions:

• chr2-187598966-G-A
• chr2-187598966-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 0.138 in 151,698 control chromosomes in the GnomAD database, including 1,669 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 0.14 (1669 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20977 AN: 151582 Hom.: 1668 Cov.: 29

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.138 AC: 20985 AN: 151698 Hom.: 1669 Cov.: 29 AF XY: 0.143 AC XY: 10635 AN XY: 74124

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0406 Hom.: 34

Bravo AF: 0.143

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.7
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4666734; hg19: chr2-188463693;