rs1388240

Positions:

• chr4-126736287-C-A
• chr4-126736287-C-G

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 0.319 in 151,952 control chromosomes in the GnomAD database, including 7,974 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 0.32 (7974 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.126736287C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48453 AN: 151834 Hom.: 7971 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.319 AC: 48466 AN: 151952 Hom.: 7974 Cov.: 32 AF XY: 0.322 AC XY: 23934 AN XY: 74254

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.325

Alfa AF: 0.326 Hom.: 16733

Bravo AF: 0.306

Asia WGS AF: 0.414 AC: 1434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1388240; hg19: chr4-127657442;