rs480092

Positions:

• chr6-31797122-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 0.237 in 152,036 control chromosomes in the GnomAD database, including 4,806 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 0.24 (4806 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.237 AC: 35943 AN: 151918 Hom.: 4802 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.237 AC: 35981 AN: 152036 Hom.: 4806 Cov.: 31 AF XY: 0.245 AC XY: 18209 AN XY: 74290

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.208

Alfa AF: 0.178 Hom.: 3400

Bravo AF: 0.233

Asia WGS AF: 0.263 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs480092; hg19: chr6-31764899;