5-119433779-A-T

Position:

• chr5-119433779-A-T

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 0.115 in 152,248 control chromosomes in the GnomAD database, including 1,278 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 0.12 (1278 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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: 0.115 AC: 17517 AN: 152132 Hom.: 1273 Cov.: 33

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.115 AC: 17521 AN: 152248 Hom.: 1278 Cov.: 33 AF XY: 0.120 AC XY: 8959 AN XY: 74434

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0700

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.114

Alfa AF: 0.132 Hom.: 210

Bravo AF: 0.102

Asia WGS AF: 0.175 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs384346; hg19: chr5-118769474; COSMIC: COSV60187223;