rs7689267

Positions:

• chr4-117004426-C-G

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 0.0756 in 152,018 control chromosomes in the GnomAD database, including 696 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 0.076 (696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 11477 AN: 151900 Hom.: 693 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0756 AC: 11492 AN: 152018 Hom.: 696 Cov.: 32 AF XY: 0.0775 AC XY: 5759 AN XY: 74310

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.0274

Gnomad4 SAS AF: 0.0997

Gnomad4 FIN AF: 0.0232

Gnomad4 NFE AF: 0.0347

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0574 Hom.: 54

Bravo AF: 0.0880

Asia WGS AF: 0.0700 AC: 241 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.025
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7689267; hg19: chr4-117925582;