5-85287951-G-T

Variant names:

• chr5-85287951-G-T
• rs12153606

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 0.131 in 152,096 control chromosomes in the GnomAD database, including 1,666 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 0.13 (1666 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19909 AN: 151978 Hom.: 1665 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.131 AC: 19927 AN: 152096 Hom.: 1666 Cov.: 32 AF XY: 0.128 AC XY: 9517 AN XY: 74334

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.144

Alfa AF: 0.158 Hom.: 260

Bravo AF: 0.124

Asia WGS AF: 0.0860 AC: 301 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12153606; hg19: chr5-84583769; COSMIC: COSV51332599;