5-143266338-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 0.883 in 151,826 control chromosomes in the GnomAD database, including 59,618 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 0.88 (59618 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 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: 0.883 AC: 134030 AN: 151708 Hom.: 59586 Cov.: 29

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.883 AC: 134111 AN: 151826 Hom.: 59618 Cov.: 29 AF XY: 0.881 AC XY: 65382 AN XY: 74226

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.894

Alfa AF: 0.923 Hom.: 83923

Bravo AF: 0.872

Asia WGS AF: 0.804 AC: 2795 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	5.2
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs244465; hg19: chr5-142645903;