rs7689267

Variant names:

• chr4-117004426-C-G
• rs7689267

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 0.0756 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.128 AC: 5315 AN: 41486

American (AMR) AF: 0.164 AC: 2498 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3468

East Asian (EAS) AF: 0.0274 AC: 141 AN: 5152

South Asian (SAS) AF: 0.0997 AC: 481 AN: 4824

European-Finnish (FIN) AF: 0.0232 AC: 245 AN: 10574

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0347 AC: 2360 AN: 67968

Other (OTH) AF: 0.0659 AC: 139 AN: 2110

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7689267; hg19: chr4-117925582;