rs12200560

Variant names:

• chr6-96632322-A-G
• rs12200560

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 0.365 in 152,036 control chromosomes in the GnomAD database, including 11,888 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 (11888 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

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 = 0.493 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: 0.365 AC: 55469 AN: 151918 Hom.: 11895 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.365 AC: 55444 AN: 152036 Hom.: 11888 Cov.: 32 AF XY: 0.361 AC XY: 26841 AN XY: 74328

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.390

Alfa AF: 0.479 Hom.: 28587

Bravo AF: 0.352

Asia WGS AF: 0.271 AC: 947 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	3.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12200560; hg19: chr6-97080198;