rs1027560

Variant names:

• chr12-130120191-G-A
• rs1027560

Your query was ambiguous. Multiple possible variants found:

• chr12-130120191-G-A
• chr12-130120191-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.564 AC: 23293 AN: 41318

American (AMR) AF: 0.452 AC: 6882 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3578 AN: 5076

South Asian (SAS) AF: 0.510 AC: 2459 AN: 4820

European-Finnish (FIN) AF: 0.431 AC: 4540 AN: 10544

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24682 AN: 67830

Other (OTH) AF: 0.411 AC: 866 AN: 2108

Alfa AF: 0.390 Hom.: 37021

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1027560; hg19: chr12-130604736;