rs1027560

Positions:

• chr12-130120191-G-A
• chr12-130120191-G-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 0.448 in 151,596 control chromosomes in the GnomAD database, including 15,944 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 0.45 (15944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67897 AN: 151478 Hom.: 15915 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.448 AC: 67973 AN: 151596 Hom.: 15944 Cov.: 32 AF XY: 0.454 AC XY: 33644 AN XY: 74066

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.411

Alfa AF: 0.375 Hom.: 21733

Bravo AF: 0.457

Asia WGS AF: 0.580 AC: 2013 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1027560; hg19: chr12-130604736;