4-186093935-C-T

Variant names:

• chr4-186093935-C-T
• rs1519309

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 0.583 in 152,116 control chromosomes in the GnomAD database, including 27,101 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 0.58 (27101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.584 AC: 88691 AN: 151998 Hom.: 27091 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.583 AC: 88739 AN: 152116 Hom.: 27101 Cov.: 32 AF XY: 0.592 AC XY: 43990 AN XY: 74360

African (AFR) AF: 0.395 AC: 16400 AN: 41498

American (AMR) AF: 0.635 AC: 9701 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1805 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3615 AN: 5164

South Asian (SAS) AF: 0.604 AC: 2914 AN: 4824

European-Finnish (FIN) AF: 0.784 AC: 8294 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 44001 AN: 67990

Other (OTH) AF: 0.590 AC: 1243 AN: 2108

Alfa AF: 0.621 Hom.: 102320

Bravo AF: 0.565

Asia WGS AF: 0.607 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.46
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1519309; hg19: chr4-187015089;