rs4665777

Variant names:

• chr2-25188027-C-T
• rs4665777

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 0.212 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
• Publications: 4 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.208 AC: 8616 AN: 41476

American (AMR) AF: 0.348 AC: 5309 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5176

South Asian (SAS) AF: 0.158 AC: 762 AN: 4812

European-Finnish (FIN) AF: 0.282 AC: 2986 AN: 10580

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12430 AN: 67990

Other (OTH) AF: 0.200 AC: 422 AN: 2110

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4665777; hg19: chr2-25410896;