rs2251212

chr20-45414588-G-Achr20-45414588-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC107985405 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985405	XR_001754640.2	n.2400C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.0882

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.128

Alfa AF: 0.133 Hom.: 1555

Bravo AF: 0.170

Asia WGS AF: 0.269 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.5
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251212; hg19: chr20-44043228;