chr5-99445399-C-T

Position:

• chr5-99445399-C-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 0.394 in 151,936 control chromosomes in the GnomAD database, including 12,039 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 0.39 (12039 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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: 0.394 AC: 59772 AN: 151818 Hom.: 12020 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.394 AC: 59833 AN: 151936 Hom.: 12039 Cov.: 32 AF XY: 0.397 AC XY: 29481 AN XY: 74250

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.404

Alfa AF: 0.411 Hom.: 18278

Bravo AF: 0.383

Asia WGS AF: 0.366 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1829883; hg19: chr5-98781103;