rs2251212

Variant names:

• chr20-45414588-G-A
• rs2251212
• XR_001754640.2:n.2400C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-45414588-G-A
• chr20-45414588-G-T

Variant summary

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

The XR_001754640.2(LOC107985405):​n.2400C>T 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 0.163 in 151,980 control chromosomes in the GnomAD database, including 2,330 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 0.16 (2330 hom., cov: 32)
• Consequence: LOC107985405 XR_001754640.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645
• Publications: 7 publications found

Genes affected

LOC107985405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.291 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: 0.163 AC: 24735 AN: 151862 Hom.: 2327 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.0882

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.163 AC: 24756 AN: 151980 Hom.: 2330 Cov.: 32 AF XY: 0.168 AC XY: 12448 AN XY: 74286

African (AFR) AF: 0.201 AC: 8313 AN: 41384

American (AMR) AF: 0.211 AC: 3227 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1495 AN: 5178

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4818

European-Finnish (FIN) AF: 0.0882 AC: 929 AN: 10538

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8432 AN: 67978

Other (OTH) AF: 0.128 AC: 271 AN: 2114

Alfa AF: 0.137 Hom.: 4312

Bravo AF: 0.170

Asia WGS AF: 0.269 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5
DANN	Benign	0.76
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs2251212; hg19: chr20-44043228;