rs1499111

chr4-128551184-C-T

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 0.255 in 152,048 control chromosomes in the GnomAD database, including 5,646 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 0.26 (5646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

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 (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38740 AN: 151930 Hom.: 5628 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.255 AC: 38801 AN: 152048 Hom.: 5646 Cov.: 32 AF XY: 0.254 AC XY: 18872 AN XY: 74340

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0569

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.259

Alfa AF: 0.217 Hom.: 1958

Bravo AF: 0.261

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.9
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1499111; hg19: chr4-129472339;