10-44398308-C-T

Position:

• chr10-44398308-C-T

Variant summary

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

The XR_001747298.2(LOC107984179):​n.188+31C>T 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 0.555 in 152,110 control chromosomes in the GnomAD database, including 26,216 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 0.55 (26216 hom., cov: 33)
• Consequence: LOC107984179 XR_001747298.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.188+31C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84372 AN: 151992 Hom.: 26210 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.555 AC: 84397 AN: 152110 Hom.: 26216 Cov.: 33 AF XY: 0.562 AC XY: 41787 AN XY: 74368

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.588

Alfa AF: 0.638 Hom.: 16876

Bravo AF: 0.538

Asia WGS AF: 0.655 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023264; hg19: chr10-44893756;