5-143266338-T-C

Variant names:

• chr5-143266338-T-C
• rs244465

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;