rs7659024

chr4-154599778-G-Achr4-154599778-G-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 0.265 in 151,902 control chromosomes in the GnomAD database, including 5,583 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 0.26 (5583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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 (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.265 AC: 40167 AN: 151784 Hom.: 5573 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.265 AC: 40210 AN: 151902 Hom.: 5583 Cov.: 32 AF XY: 0.267 AC XY: 19828 AN XY: 74246

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.225

Alfa AF: 0.233 Hom.: 9014

Bravo AF: 0.262

Asia WGS AF: 0.317 AC: 1094 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.0
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7659024; hg19: chr4-155520930;