rs10900020

Positions:

• chr10-44331749-A-T

Variant summary

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

The XR_007062369.1(LOC124902544):​n.3742+15799T>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 0.0912 in 152,274 control chromosomes in the GnomAD database, including 827 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 0.091 (827 hom., cov: 33)
• Consequence: LOC124902544 XR_007062369.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LOC124902544 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902544	XR_007062369.1	n.3742+15799T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13871 AN: 152156 Hom.: 828 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0745

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0912 AC: 13885 AN: 152274 Hom.: 827 Cov.: 33 AF XY: 0.0886 AC XY: 6595 AN XY: 74454

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0623

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0745

Gnomad4 NFE AF: 0.0716

Gnomad4 OTH AF: 0.0912

Alfa AF: 0.0850 Hom.: 86

Bravo AF: 0.0959

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.80
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10900020; hg19: chr10-44827197;