rs1986513

chr4-125146073-A-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 0.0912 in 152,180 control chromosomes in the GnomAD database, including 845 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 0.091 (845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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: 0.0911 AC: 13848 AN: 152062 Hom.: 842 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0941

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.0751

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

GnomAD4 genome AF: 0.0912 AC: 13872 AN: 152180 Hom.: 845 Cov.: 32 AF XY: 0.0944 AC XY: 7022 AN XY: 74392

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0941

Gnomad4 NFE AF: 0.0553

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0780 Hom.: 79

Bravo AF: 0.0947

Asia WGS AF: 0.189 AC: 655 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.5
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1986513; hg19: chr4-126067228;