rs482180

Variant names:

• chr6-23925552-T-C
• rs482180

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 0.141 in 152,124 control chromosomes in the GnomAD database, including 2,029 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 0.14 (2029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.865

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 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: 0.141 AC: 21447 AN: 152006 Hom.: 2029 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00384

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.0909

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.141 AC: 21456 AN: 152124 Hom.: 2029 Cov.: 32 AF XY: 0.137 AC XY: 10219 AN XY: 74374

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00385

Gnomad4 SAS AF: 0.0568

Gnomad4 FIN AF: 0.0909

Gnomad4 NFE AF: 0.0997

Gnomad4 OTH AF: 0.138

Alfa AF: 0.132 Hom.: 178

Bravo AF: 0.148

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs482180; hg19: chr6-23925780;