5-100907801-T-C

Position:

• chr5-100907801-T-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 0.23 in 152,132 control chromosomes in the GnomAD database, including 5,058 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 (5058 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357

Genes affected

(HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100907801T>C		intergenic_region
LOC107986437	XR_001742825.3	n.2262+2132T>C		intron_variant
LOC107986437	XR_001742826.3	n.2262+2132T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.230 AC: 35023 AN: 152014 Hom.: 5057 Cov.: 32

Gnomad AFR AF: 0.0656

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.230 AC: 35011 AN: 152132 Hom.: 5058 Cov.: 32 AF XY: 0.232 AC XY: 17265 AN XY: 74362

Gnomad4 AFR AF: 0.0654

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.236

Alfa AF: 0.255 Hom.: 892

Bravo AF: 0.214

Asia WGS AF: 0.171 AC: 597 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1833862; hg19: chr5-100243505;