chr4-129523677-A-G

Variant names:

• chr4-129523677-A-G
• rs724156

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 0.273 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.235 AC: 9765 AN: 41506

American (AMR) AF: 0.251 AC: 3832 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1359 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1619 AN: 5158

South Asian (SAS) AF: 0.339 AC: 1637 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3291 AN: 10588

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.281 AC: 19091 AN: 67988

Other (OTH) AF: 0.300 AC: 632 AN: 2108

Alfa AF: 0.281 Hom.: 10356

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs724156; hg19: chr4-130444832;