rs12653736

chr5-111064929-G-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 0.0409 in 152,194 control chromosomes in the GnomAD database, including 188 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 0.041 (188 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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: 0.0408 AC: 6211 AN: 152076 Hom.: 186 Cov.: 33

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0756

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0274

Gnomad OTH AF: 0.0532

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

GnomAD4 genome AF: 0.0409 AC: 6227 AN: 152194 Hom.: 188 Cov.: 33 AF XY: 0.0415 AC XY: 3090 AN XY: 74388

Gnomad4 AFR AF: 0.0537

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.0326

Gnomad4 NFE AF: 0.0274

Gnomad4 OTH AF: 0.0546

Alfa AF: 0.0295 Hom.: 78

Bravo AF: 0.0384

Asia WGS AF: 0.123 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.56
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12653736; hg19: chr5-110400627;