rs2480

Positions:

• chr6-16113502-C-T

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 0.604 in 152,042 control chromosomes in the GnomAD database, including 30,096 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 0.60 (30096 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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 (AFR) allele frequency at 95% confidence interval = 0.863 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: 0.603 AC: 91643 AN: 151924 Hom.: 30035 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.604 AC: 91762 AN: 152042 Hom.: 30096 Cov.: 32 AF XY: 0.599 AC XY: 44528 AN XY: 74320

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.569

Alfa AF: 0.493 Hom.: 36061

Bravo AF: 0.631

Asia WGS AF: 0.665 AC: 2312 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	1.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2480; hg19: chr6-16113733;