rs169902

Variant names:

• chr7-52585050-C-T
• rs169902

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 0.525 in 152,106 control chromosomes in the GnomAD database, including 21,484 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 0.53 (21484 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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: 0.525 AC: 79834 AN: 151988 Hom.: 21447 Cov.: 33

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.525 AC: 79927 AN: 152106 Hom.: 21484 Cov.: 33 AF XY: 0.521 AC XY: 38733 AN XY: 74336

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.512

Alfa AF: 0.489 Hom.: 10824

Bravo AF: 0.537

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.087
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169902; hg19: chr7-52652746;