5-4029676-C-T

Variant names:

• chr5-4029676-C-T
• rs11748327

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 0.212 in 152,106 control chromosomes in the GnomAD database, including 3,994 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 (3994 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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: 0.212 AC: 32188 AN: 151988 Hom.: 3990 Cov.: 33

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.212 AC: 32200 AN: 152106 Hom.: 3994 Cov.: 33 AF XY: 0.208 AC XY: 15472 AN XY: 74340

Gnomad4 AFR AF: 0.0929

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.236

Alfa AF: 0.272 Hom.: 2247

Bravo AF: 0.206

Asia WGS AF: 0.190 AC: 660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11748327; hg19: chr5-4029789;