10-46200833-A-G

Variant names:

• chr10-46200833-A-G
• rs11259816
• XR_007062137.1:n.2241T>C

Variant summary

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

The XR_007062137.1(LOC124902418):​n.2241T>C 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 0.4 in 151,310 control chromosomes in the GnomAD database, including 11,967 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 0.40 (11967 hom., cov: 32)
• Consequence: LOC124902418 XR_007062137.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

Genes affected

LOC124902418 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902418	XR_007062137.1	n.2241T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60406 AN: 151200 Hom.: 11954 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.400 AC: 60451 AN: 151310 Hom.: 11967 Cov.: 32 AF XY: 0.403 AC XY: 29785 AN XY: 73970

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.399

Alfa AF: 0.209 Hom.: 383

Bravo AF: 0.412

Asia WGS AF: 0.452 AC: 1570 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11259816; hg19: chr10-47572069;