rs480092

Variant names:

• chr6-31797122-T-C
• rs480092

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 42 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.326 AC: 13534 AN: 41460

American (AMR) AF: 0.264 AC: 4024 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5168

South Asian (SAS) AF: 0.249 AC: 1203 AN: 4822

European-Finnish (FIN) AF: 0.364 AC: 3837 AN: 10552

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11458 AN: 67994

Other (OTH) AF: 0.208 AC: 438 AN: 2110

Alfa AF: 0.188 Hom.: 10653

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs480092; hg19: chr6-31764899;