rs60905866

chr5-112696878-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 0.059 in 152,188 control chromosomes in the GnomAD database, including 532 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 0.059 (532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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 (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.0590 AC: 8970 AN: 152070 Hom.: 529 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.00604

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0590 AC: 8982 AN: 152188 Hom.: 532 Cov.: 32 AF XY: 0.0595 AC XY: 4423 AN XY: 74386

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0303

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.00604

Gnomad4 NFE AF: 0.0195

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.0305 Hom.: 81

Bravo AF: 0.0651

Asia WGS AF: 0.114 AC: 396 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	4.3
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60905866; hg19: chr5-112032575;