rs1986513

Variant names:

• chr4-125146073-A-T
• rs1986513

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 0.0912 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.119 AC: 4949 AN: 41514

American (AMR) AF: 0.102 AC: 1558 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 439 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5176

South Asian (SAS) AF: 0.136 AC: 654 AN: 4824

European-Finnish (FIN) AF: 0.0941 AC: 999 AN: 10614

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0553 AC: 3763 AN: 67994

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1986513; hg19: chr4-126067228;