rs4128714

Variant names:

• chr11-5173434-T-C
• rs4128714

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 0.205 in 152,006 control chromosomes in the GnomAD database, including 3,554 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 0.21 (3554 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 3 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 = 0.244 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: 0.205 AC: 31199 AN: 151888 Hom.: 3550 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.205 AC: 31224 AN: 152006 Hom.: 3554 Cov.: 33 AF XY: 0.205 AC XY: 15230 AN XY: 74298

African (AFR) AF: 0.136 AC: 5642 AN: 41496

American (AMR) AF: 0.250 AC: 3818 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5188

South Asian (SAS) AF: 0.249 AC: 1202 AN: 4820

European-Finnish (FIN) AF: 0.207 AC: 2188 AN: 10566

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16584 AN: 67896

Other (OTH) AF: 0.236 AC: 497 AN: 2110

Alfa AF: 0.216 Hom.: 1241

Bravo AF: 0.206

Asia WGS AF: 0.156 AC: 541 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4128714; hg19: chr11-5194664;