rs10826304

chr10-59510907-G-Achr10-59510907-G-C

Variant summary

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

The XR_001747457.1(LOC107984235):n.84+27807C>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 0.396 in 152,026 control chromosomes in the GnomAD database, including 13,317 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 0.40 (13317 hom., cov: 32)
• Consequence: LOC107984235 XR_001747457.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

Genes affected

LOC107984235 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984235	XR_001747457.1	n.84+27807C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60263 AN: 151908 Hom.: 13323 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.396 AC: 60260 AN: 152026 Hom.: 13317 Cov.: 32 AF XY: 0.398 AC XY: 29562 AN XY: 74278

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.451

Alfa AF: 0.338 Hom.: 1442

Bravo AF: 0.380

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.4
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10826304; hg19: chr10-61270665; COSMIC: COSV56522401;