chr4-117172468-T-C

Variant names:

• chr4-117172468-T-C
• rs11098380

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 0.491 in 151,578 control chromosomes in the GnomAD database, including 18,863 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 0.49 (18863 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.663 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: 0.491 AC: 74432 AN: 151460 Hom.: 18843 Cov.: 30

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.491 AC: 74469 AN: 151578 Hom.: 18863 Cov.: 30 AF XY: 0.494 AC XY: 36598 AN XY: 74034

African (AFR) AF: 0.411 AC: 16979 AN: 41360

American (AMR) AF: 0.674 AC: 10235 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1454 AN: 3460

East Asian (EAS) AF: 0.436 AC: 2232 AN: 5116

South Asian (SAS) AF: 0.468 AC: 2243 AN: 4792

European-Finnish (FIN) AF: 0.531 AC: 5594 AN: 10530

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34149 AN: 67818

Other (OTH) AF: 0.510 AC: 1075 AN: 2106

Alfa AF: 0.511 Hom.: 33366

Bravo AF: 0.502

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.84
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11098380; hg19: chr4-118093624;