10-91774867-T-C

Position:

• chr10-91774867-T-C

Variant summary

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

The XR_007062246.1(LOC124902482):​n.216+2397T>C 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 0.484 in 152,118 control chromosomes in the GnomAD database, including 18,718 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 0.48 (18718 hom., cov: 32)
• Consequence: LOC124902482 XR_007062246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

Genes affected

LOC124902482 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902482	XR_007062246.1	n.216+2397T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73583 AN: 152000 Hom.: 18701 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.484 AC: 73644 AN: 152118 Hom.: 18718 Cov.: 32 AF XY: 0.499 AC XY: 37077 AN XY: 74372

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.453

Alfa AF: 0.438 Hom.: 19531

Bravo AF: 0.475

Asia WGS AF: 0.724 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1361552; hg19: chr10-93534624;