rs7690467

chr4-132405240-T-C

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 0.34 in 151,820 control chromosomes in the GnomAD database, including 9,216 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 0.34 (9216 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 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: 0.340 AC: 51537 AN: 151702 Hom.: 9173 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.340 AC: 51645 AN: 151820 Hom.: 9216 Cov.: 31 AF XY: 0.343 AC XY: 25466 AN XY: 74182

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.337

Alfa AF: 0.310 Hom.: 3944

Bravo AF: 0.357

Asia WGS AF: 0.386 AC: 1332 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.34
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7690467; hg19: chr4-133326395;