rs480110

Variant names:

• chr6-145084898-A-G
• rs480110

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 0.398 in 152,014 control chromosomes in the GnomAD database, including 14,150 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 0.40 (14150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 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: 0.398 AC: 60478 AN: 151896 Hom.: 14150 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.398 AC: 60480 AN: 152014 Hom.: 14150 Cov.: 32 AF XY: 0.395 AC XY: 29345 AN XY: 74288

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.402

Alfa AF: 0.486 Hom.: 10628

Bravo AF: 0.380

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs480110; hg19: chr6-145406034; COSMIC: COSV60289952;