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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373602	XR_001739693.1	n.210+23301G>T		intron_variant	Intron 2 of 2
LOC105373602	XR_001739694.1	n.211-9450G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;