rs10207651

Variant names:

• chr2-126609649-C-A
• rs10207651
• XR_001739693.1:n.210+23301G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-126609649-C-A
• chr2-126609649-C-T

Variant summary

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

The XR_001739693.1(LOC105373602):​n.210+23301G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,152 control chromosomes in the GnomAD database, including 6,054 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 0.28 (6054 hom., cov: 32)
• Consequence: LOC105373602 XR_001739693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• Publications: 0 publications found

Genes affected

LOC105373602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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: 0.282 AC: 42548 AN: 151032 Hom.: 6054 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.282 AC: 42563 AN: 151152 Hom.: 6054 Cov.: 32 AF XY: 0.280 AC XY: 20673 AN XY: 73808

African (AFR) AF: 0.266 AC: 10992 AN: 41356

American (AMR) AF: 0.235 AC: 3555 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1091 AN: 3454

East Asian (EAS) AF: 0.130 AC: 667 AN: 5150

South Asian (SAS) AF: 0.199 AC: 958 AN: 4812

European-Finnish (FIN) AF: 0.308 AC: 3199 AN: 10400

Middle Eastern (MID) AF: 0.342 AC: 95 AN: 278

European-Non Finnish (NFE) AF: 0.311 AC: 20985 AN: 67564

Other (OTH) AF: 0.286 AC: 600 AN: 2096

Alfa AF: 0.298 Hom.: 1090

Bravo AF: 0.274

Asia WGS AF: 0.151 AC: 517 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	6.4
DANN	Benign	0.86
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs10207651; hg19: chr2-127367226;