rs11200630

Positions:

• chr10-122450168-T-C
• chr10-122450168-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_946382.3(LOC105378525):​n.2646A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,166 control chromosomes in the GnomAD database, including 3,966 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 0.22 (3966 hom., cov: 32)
• Consequence: LOC105378525 XR_946382.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

LOC105378525 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378525	XR_946382.3	n.2646A>G		non_coding_transcript_exon_variant	3/3
LOC105378525	XR_946383.3	n.2449A>G		non_coding_transcript_exon_variant	4/4
LOC105378525	XR_946384.3	n.2373A>G		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650300.1	n.1852+8327A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33787 AN: 152048 Hom.: 3960 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.222 AC: 33820 AN: 152166 Hom.: 3966 Cov.: 32 AF XY: 0.225 AC XY: 16739 AN XY: 74370

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.227

Alfa AF: 0.181 Hom.: 652

Bravo AF: 0.223

Asia WGS AF: 0.363 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11200630; hg19: chr10-124209684;