rs7659024

Variant names:

• chr4-154599778-G-A
• rs7659024

Your query was ambiguous. Multiple possible variants found:

• chr4-154599778-G-A
• chr4-154599778-G-C

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 0.265 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
• Publications: 28 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.298 AC: 12326 AN: 41410

American (AMR) AF: 0.222 AC: 3388 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2307 AN: 5176

South Asian (SAS) AF: 0.295 AC: 1418 AN: 4814

European-Finnish (FIN) AF: 0.297 AC: 3123 AN: 10518

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16397 AN: 67932

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.240 Hom.: 14660

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7659024; hg19: chr4-155520930;