rs4128714

chr11-5173434-T-C

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 0.205 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.236

Alfa AF: 0.223 Hom.: 631

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128714; hg19: chr11-5194664;