2-222746080-C-T

Variant names:

• chr2-222746080-C-T
• rs959327
• XR_001739904.2:n.570-4073C>T

Variant summary

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

The XR_001739904.2(LOC105373903):​n.570-4073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,082 control chromosomes in the GnomAD database, including 18,175 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 0.48 (18175 hom., cov: 32)
• Consequence: LOC105373903 XR_001739904.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 5 publications found

Genes affected

LOC105373903 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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: 0.484 AC: 73548 AN: 151964 Hom.: 18162 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.484 AC: 73594 AN: 152082 Hom.: 18175 Cov.: 32 AF XY: 0.489 AC XY: 36347 AN XY: 74354

African (AFR) AF: 0.403 AC: 16702 AN: 41480

American (AMR) AF: 0.483 AC: 7372 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1812 AN: 3466

East Asian (EAS) AF: 0.798 AC: 4141 AN: 5188

South Asian (SAS) AF: 0.595 AC: 2871 AN: 4824

European-Finnish (FIN) AF: 0.538 AC: 5682 AN: 10566

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33363 AN: 67968

Other (OTH) AF: 0.491 AC: 1038 AN: 2114

Alfa AF: 0.490 Hom.: 77076

Bravo AF: 0.477

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.77
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs959327; hg19: chr2-223610799;