10-121121873-A-T

Position:

• chr10-121121873-A-T

Variant summary

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

The XR_007062318.1(LOC124902515):​n.159-2524T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,270 control chromosomes in the GnomAD database, including 1,529 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 0.13 (1529 hom., cov: 33)
• Consequence: LOC124902515 XR_007062318.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

Genes affected

LOC124902515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902515	XR_007062318.1	n.159-2524T>A		intron_variant, non_coding_transcript_variant
LOC124902515	XR_007062317.1	n.168-2524T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19299 AN: 152152 Hom.: 1528 Cov.: 33

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.127 AC: 19306 AN: 152270 Hom.: 1529 Cov.: 33 AF XY: 0.127 AC XY: 9439 AN XY: 74440

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0971

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.153

Alfa AF: 0.132 Hom.: 208

Bravo AF: 0.123

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12771493; hg19: chr10-122881387;