rs9291531

Variant names:

• chr4-29880004-A-T
• rs9291531

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 0.0801 in 151,920 control chromosomes in the GnomAD database, including 1,235 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 0.080 (1235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.0801 AC: 12156 AN: 151802 Hom.: 1236 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.00693

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0801 AC: 12166 AN: 151920 Hom.: 1235 Cov.: 32 AF XY: 0.0801 AC XY: 5950 AN XY: 74252

African (AFR) AF: 0.227 AC: 9413 AN: 41394

American (AMR) AF: 0.0472 AC: 719 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.167 AC: 860 AN: 5150

South Asian (SAS) AF: 0.0495 AC: 238 AN: 4808

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10602

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.00692 AC: 470 AN: 67942

Other (OTH) AF: 0.0719 AC: 152 AN: 2114

Alfa AF: 0.0487 Hom.: 85

Bravo AF: 0.0904

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.42
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs9291531; hg19: chr4-29881626;