rs12733856

Variant names:

• chr1-221378197-C-A
• rs12733856
• XR_922621.2:n.455-1565C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-221378197-C-A
• chr1-221378197-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_922621.2(LOC105372932):​n.455-1565C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,946 control chromosomes in the GnomAD database, including 7,963 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 0.30 (7963 hom., cov: 32)
• Consequence: LOC105372932 XR_922621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 12 publications found

Genes affected

LOC105372932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45859 AN: 151828 Hom.: 7968 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.302 AC: 45871 AN: 151946 Hom.: 7963 Cov.: 32 AF XY: 0.307 AC XY: 22826 AN XY: 74258

African (AFR) AF: 0.401 AC: 16617 AN: 41418

American (AMR) AF: 0.352 AC: 5361 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3468

East Asian (EAS) AF: 0.653 AC: 3370 AN: 5164

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4810

European-Finnish (FIN) AF: 0.237 AC: 2505 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14415 AN: 67968

Other (OTH) AF: 0.277 AC: 583 AN: 2108

Alfa AF: 0.252 Hom.: 16276

Bravo AF: 0.317

Asia WGS AF: 0.493 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.32
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12733856; hg19: chr1-221551539;