5-103284973-A-G

Position:

• chr5-103284973-A-G

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 0.114 in 152,136 control chromosomes in the GnomAD database, including 2,035 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 0.11 (2035 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.103284973A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17225 AN: 152018 Hom.: 2017 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.114 AC: 17300 AN: 152136 Hom.: 2035 Cov.: 32 AF XY: 0.112 AC XY: 8296 AN XY: 74390

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.0356

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0953

Alfa AF: 0.0371 Hom.: 56

Bravo AF: 0.131

Asia WGS AF: 0.0640 AC: 223 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.29
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10079088; hg19: chr5-102620674;