rs724156

Variant names:

• chr4-129523677-A-G
• rs724156

Your query was ambiguous. Multiple possible variants found:

• chr4-129523677-A-G
• chr4-129523677-A-T

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 0.273 in 152,130 control chromosomes in the GnomAD database, including 5,813 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 0.27 (5813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 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: 0.273 AC: 41503 AN: 152012 Hom.: 5813 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.273 AC: 41510 AN: 152130 Hom.: 5813 Cov.: 32 AF XY: 0.275 AC XY: 20458 AN XY: 74364

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.300

Alfa AF: 0.282 Hom.: 8219

Bravo AF: 0.271

Asia WGS AF: 0.278 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
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: rs724156; hg19: chr4-130444832;