XR_923311.4:n.671+1716T>C

Variant names:

• chr2-127109531-T-C
• rs9653202
• XR_923311.4:n.671+1716T>C

Variant summary

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

The XR_923311.4(LOC105373605):​n.671+1716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0843 in 152,252 control chromosomes in the GnomAD database, including 722 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 0.084 (722 hom., cov: 33)
• Consequence: LOC105373605 XR_923311.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650
• Publications: 4 publications found

Genes affected

LOC105373605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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: 0.0840 AC: 12785 AN: 152134 Hom.: 714 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.0885

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0843 AC: 12828 AN: 152252 Hom.: 722 Cov.: 33 AF XY: 0.0836 AC XY: 6224 AN XY: 74450

African (AFR) AF: 0.156 AC: 6473 AN: 41534

American (AMR) AF: 0.0610 AC: 933 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.0606 AC: 314 AN: 5184

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4822

European-Finnish (FIN) AF: 0.0288 AC: 306 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3847 AN: 68020

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0748 Hom.: 81

Bravo AF: 0.0884

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	17
DANN	Benign	0.72
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs9653202; hg19: chr2-127867107;