2-234605853-A-G

Variant names:

• chr2-234605853-A-G
• rs869214
• XR_923998.3:n.477-8043T>C

Variant summary

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

The XR_923998.3(LOC105373936):​n.477-8043T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,728 control chromosomes in the GnomAD database, including 33,835 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 0.66 (33835 hom., cov: 30)
• Consequence: LOC105373936 XR_923998.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 4 publications found

Genes affected

LOC105373936 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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: 0.655 AC: 99307 AN: 151608 Hom.: 33799 Cov.: 30

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.655 AC: 99396 AN: 151728 Hom.: 33835 Cov.: 30 AF XY: 0.651 AC XY: 48202 AN XY: 74088

African (AFR) AF: 0.852 AC: 35292 AN: 41442

American (AMR) AF: 0.616 AC: 9383 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3468

East Asian (EAS) AF: 0.735 AC: 3776 AN: 5136

South Asian (SAS) AF: 0.607 AC: 2897 AN: 4774

European-Finnish (FIN) AF: 0.495 AC: 5200 AN: 10496

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38808 AN: 67874

Other (OTH) AF: 0.654 AC: 1375 AN: 2104

Alfa AF: 0.597 Hom.: 47473

Bravo AF: 0.673

Asia WGS AF: 0.638 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs869214; hg19: chr2-235514497;