rs112730887

Positions:

• chr5-62945099-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 0.044 in 152,096 control chromosomes in the GnomAD database, including 329 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 0.044 (329 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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: 0.0438 AC: 6654 AN: 151978 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00788

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0440 AC: 6685 AN: 152096 Hom.: 329 Cov.: 32 AF XY: 0.0436 AC XY: 3239 AN XY: 74366

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0263

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0743

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.00790

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0293 Hom.: 19

Bravo AF: 0.0478

Asia WGS AF: 0.0880 AC: 305 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	0.21
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112730887; hg19: chr5-62240926;