5-85287951-G-T

Position:

• chr5-85287951-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 0.131 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;