10-121247512-A-G

Position:

• chr10-121247512-A-G

Variant summary

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

The variant allele was found at a frequency of 0.643 in 150,932 control chromosomes in the GnomAD database, including 31,320 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 0.64 (31320 hom., cov: 27)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.121247512A>G		intergenic_region
LOC105378523	XR_007062321.1	n.516-53902T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.643 AC: 96988 AN: 150824 Hom.: 31294 Cov.: 27

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.643 AC: 97059 AN: 150932 Hom.: 31320 Cov.: 27 AF XY: 0.644 AC XY: 47408 AN XY: 73640

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.635

Alfa AF: 0.632 Hom.: 15505

Bravo AF: 0.645

Asia WGS AF: 0.742 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2901290; hg19: chr10-123007026;