chr5-100308375-A-C

Position:

• chr5-100308375-A-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 0.232 in 151,918 control chromosomes in the GnomAD database, including 4,407 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 0.23 (4407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 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: 0.232 AC: 35190 AN: 151800 Hom.: 4398 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.0184

Gnomad SAS AF: 0.0958

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.232 AC: 35237 AN: 151918 Hom.: 4407 Cov.: 32 AF XY: 0.228 AC XY: 16965 AN XY: 74250

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.0963

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.266

Alfa AF: 0.258 Hom.: 922

Bravo AF: 0.247

Asia WGS AF: 0.0840 AC: 295 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1824780; hg19: chr5-99644079;