rs1859441

Variant names:

• chr12-48029450-C-T
• rs1859441
• XR_001749115.3:n.227-321C>T

Variant summary

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

The XR_944904.3(LOC105369750):​n.227-321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,234 control chromosomes in the GnomAD database, including 3,781 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 0.21 (3781 hom., cov: 33)
• Consequence: LOC105369750 XR_944904.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 8 publications found

Genes affected

LOC105369750 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 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: 0.208 AC: 31584 AN: 152118 Hom.: 3775 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.208 AC: 31620 AN: 152234 Hom.: 3781 Cov.: 33 AF XY: 0.215 AC XY: 16019 AN XY: 74412

African (AFR) AF: 0.197 AC: 8200 AN: 41532

American (AMR) AF: 0.323 AC: 4936 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2347 AN: 5182

South Asian (SAS) AF: 0.302 AC: 1457 AN: 4826

European-Finnish (FIN) AF: 0.235 AC: 2487 AN: 10602

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10818 AN: 68002

Other (OTH) AF: 0.208 AC: 441 AN: 2116

Alfa AF: 0.180 Hom.: 5625

Bravo AF: 0.217

Asia WGS AF: 0.375 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.59
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1859441; hg19: chr12-48423233;