4-156706103-A-G

Variant names:

• chr4-156706103-A-G
• rs9332470

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 0.356 in 152,026 control chromosomes in the GnomAD database, including 12,133 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 0.36 (12133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 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: 0.356 AC: 54063 AN: 151908 Hom.: 12110 Cov.: 32

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.356 AC: 54132 AN: 152026 Hom.: 12133 Cov.: 32 AF XY: 0.355 AC XY: 26398 AN XY: 74318

African (AFR) AF: 0.628 AC: 26042 AN: 41440

American (AMR) AF: 0.262 AC: 4004 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2199 AN: 5162

South Asian (SAS) AF: 0.518 AC: 2495 AN: 4820

European-Finnish (FIN) AF: 0.193 AC: 2047 AN: 10598

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15727 AN: 67976

Other (OTH) AF: 0.316 AC: 663 AN: 2100

Alfa AF: 0.261 Hom.: 1245

Bravo AF: 0.371

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs9332470; hg19: chr4-157627255;