5-144043380-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant allele was found at a frequency of 0.0105 in 152,014 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.011 (0 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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: 0.0105 AC: 1598 AN: 151896 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00685

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.00885

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.00909

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

GnomAD4 genome AF: 0.0105 AC: 1598 AN: 152014 Hom.: 0 Cov.: 33 AF XY: 0.0108 AC XY: 800 AN XY: 74328

Gnomad4 AFR AF: 0.00680

Gnomad4 AMR AF: 0.00884

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00522

Gnomad4 SAS AF: 0.0156

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.0109

Gnomad4 OTH AF: 0.00900

Alfa AF: 0.00888 Hom.: 0

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.2
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs409220; hg19: chr5-143422945;