rs4669169

Variant names:

• chr2-7243407-A-C
• rs4669169

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 0.194 in 152,210 control chromosomes in the GnomAD database, including 3,663 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 0.19 (3663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.194 AC: 29459 AN: 152092 Hom.: 3656 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.194 AC: 29476 AN: 152210 Hom.: 3663 Cov.: 32 AF XY: 0.200 AC XY: 14888 AN XY: 74416

African (AFR) AF: 0.0547 AC: 2273 AN: 41552

American (AMR) AF: 0.315 AC: 4810 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1077 AN: 3472

East Asian (EAS) AF: 0.397 AC: 2054 AN: 5178

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4818

European-Finnish (FIN) AF: 0.232 AC: 2452 AN: 10584

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14596 AN: 67994

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.219 Hom.: 4940

Bravo AF: 0.194

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.2
DANN	Benign	0.57
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4669169; hg19: chr2-7383538;