chr4-130202774-G-A

Variant names:

• chr4-130202774-G-A
• rs13110934

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 0.291 in 152,040 control chromosomes in the GnomAD database, including 8,043 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 0.29 (8043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 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: 0.291 AC: 44243 AN: 151922 Hom.: 8045 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.291 AC: 44238 AN: 152040 Hom.: 8043 Cov.: 32 AF XY: 0.282 AC XY: 20992 AN XY: 74320

African (AFR) AF: 0.113 AC: 4678 AN: 41494

American (AMR) AF: 0.262 AC: 3999 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1184 AN: 3470

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5172

South Asian (SAS) AF: 0.162 AC: 779 AN: 4816

European-Finnish (FIN) AF: 0.314 AC: 3324 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28759 AN: 67928

Other (OTH) AF: 0.315 AC: 664 AN: 2110

Alfa AF: 0.336 Hom.: 1297

Bravo AF: 0.280

Asia WGS AF: 0.102 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.31
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs13110934; hg19: chr4-131123929;