rs10078714

Positions:

• chr5-175445129-A-G
• chr5-175445129-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 0.055 in 152,332 control chromosomes in the GnomAD database, including 440 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 0.055 (440 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 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: 0.0550 AC: 8377 AN: 152214 Hom.: 440 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0194

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0550 AC: 8377 AN: 152332 Hom.: 440 Cov.: 33 AF XY: 0.0558 AC XY: 4155 AN XY: 74490

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0194

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0477 Hom.: 53

Bravo AF: 0.0606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.65
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10078714; hg19: chr5-174872132;