rs4669169

Positions:

• chr2-7243407-A-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 0.194 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0547

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.222

Alfa AF: 0.225 Hom.: 3908

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4669169; hg19: chr2-7383538;