rs169902

Variant names:

• chr7-52585050-C-T
• rs169902

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 0.525 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.633 AC: 26295 AN: 41510

American (AMR) AF: 0.510 AC: 7801 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3468

East Asian (EAS) AF: 0.604 AC: 3118 AN: 5160

South Asian (SAS) AF: 0.402 AC: 1935 AN: 4816

European-Finnish (FIN) AF: 0.461 AC: 4876 AN: 10582

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32887 AN: 67966

Other (OTH) AF: 0.512 AC: 1081 AN: 2112

Alfa AF: 0.491 Hom.: 14558

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs169902; hg19: chr7-52652746;