chr5-144091362-C-A

Position:

• chr5-144091362-C-A

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 0.411 in 152,000 control chromosomes in the GnomAD database, including 14,642 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 0.41 (14642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62339 AN: 151880 Hom.: 14595 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.411 AC: 62436 AN: 152000 Hom.: 14642 Cov.: 32 AF XY: 0.408 AC XY: 30350 AN XY: 74304

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.414

Alfa AF: 0.357 Hom.: 1831

Bravo AF: 0.421

Asia WGS AF: 0.329 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904208; hg19: chr5-143470927;