rs4665777

Positions:

• chr2-25188027-C-T

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 0.212 in 152,096 control chromosomes in the GnomAD database, including 3,677 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 0.21 (3677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.34 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: 0.211 AC: 32132 AN: 151978 Hom.: 3661 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.212 AC: 32180 AN: 152096 Hom.: 3677 Cov.: 32 AF XY: 0.220 AC XY: 16341 AN XY: 74350

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.200

Alfa AF: 0.203 Hom.: 398

Bravo AF: 0.220

Asia WGS AF: 0.194 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	10
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4665777; hg19: chr2-25410896;