rs754618

Positions:

• chr10-44390758-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.67+926C>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 0.266 in 152,096 control chromosomes in the GnomAD database, including 6,288 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 0.27 (6288 hom., cov: 31)
• Consequence: LOC107984179 XR_001747298.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334

Genes affected

LOC107984179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984179	XR_001747298.2	n.67+926C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40385 AN: 151976 Hom.: 6288 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.266 AC: 40391 AN: 152096 Hom.: 6288 Cov.: 31 AF XY: 0.272 AC XY: 20232 AN XY: 74340

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.286

Alfa AF: 0.306 Hom.: 7617

Bravo AF: 0.263

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754618; hg19: chr10-44886206;