rs12970791

Variant names:

• chr18-65498567-G-T
• rs12970791
• XR_935583.2:n.211C>A

Variant summary

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

The XR_935583.2(LOC105372169):​n.211C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,318 control chromosomes in the GnomAD database, including 12,223 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 0.39 (12223 hom., cov: 31)
• Consequence: LOC105372169 XR_935583.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 3 publications found

Genes affected

LOC105372169 (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 = 0.577 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59578 AN: 151200 Hom.: 12219 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.394 AC: 59591 AN: 151318 Hom.: 12223 Cov.: 31 AF XY: 0.394 AC XY: 29103 AN XY: 73878

African (AFR) AF: 0.284 AC: 11735 AN: 41268

American (AMR) AF: 0.369 AC: 5573 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1874 AN: 3460

East Asian (EAS) AF: 0.595 AC: 3024 AN: 5084

South Asian (SAS) AF: 0.453 AC: 2171 AN: 4796

European-Finnish (FIN) AF: 0.398 AC: 4177 AN: 10490

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29534 AN: 67798

Other (OTH) AF: 0.403 AC: 848 AN: 2102

Alfa AF: 0.396 Hom.: 2089

Bravo AF: 0.392

Asia WGS AF: 0.437 AC: 1521 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	5.6
DANN	Benign	0.55
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12970791; hg19: chr18-63165803;