rs480034

Variant names:

• chr6-149414294-T-C
• rs480034

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 0.358 in 152,084 control chromosomes in the GnomAD database, including 10,102 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 0.36 (10102 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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: 0.358 AC: 54423 AN: 151966 Hom.: 10085 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.358 AC: 54474 AN: 152084 Hom.: 10102 Cov.: 31 AF XY: 0.361 AC XY: 26873 AN XY: 74340

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.392

Alfa AF: 0.373 Hom.: 1828

Bravo AF: 0.365

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0070
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs480034; hg19: chr6-149735430;