rs169642

Variant names:

• chr7-25584469-G-A
• rs169642

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 0.606 in 152,050 control chromosomes in the GnomAD database, including 28,267 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 0.61 (28267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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: 0.606 AC: 92053 AN: 151932 Hom.: 28248 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.606 AC: 92130 AN: 152050 Hom.: 28267 Cov.: 32 AF XY: 0.605 AC XY: 45002 AN XY: 74344

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.615

Alfa AF: 0.571 Hom.: 50588

Bravo AF: 0.621

Asia WGS AF: 0.690 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.88
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169642; hg19: chr7-25624089;