rs169

Variant names:

• chr7-25006722-A-G
• rs169

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 0.849 in 152,112 control chromosomes in the GnomAD database, including 55,126 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 0.85 (55126 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 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: 0.848 AC: 128949 AN: 151994 Hom.: 55059 Cov.: 29

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.849 AC: 129076 AN: 152112 Hom.: 55126 Cov.: 29 AF XY: 0.851 AC XY: 63228 AN XY: 74336

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.856

Alfa AF: 0.818 Hom.: 66958

Bravo AF: 0.857

Asia WGS AF: 0.889 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169; hg19: chr7-25046341;