rs10105219

chr8-82944940-T-C

Variant summary

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

The NR_134295.1(LOC101927141):n.361-16256T>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 0.502 in 151,762 control chromosomes in the GnomAD database, including 20,264 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 0.50 (20264 hom., cov: 33)
• Consequence: LOC101927141 NR_134295.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927141	NR_134295.1	n.361-16256T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522123.1	n.57+13700A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000663058.1	n.1029-7397T>C		intron_variant, non_coding_transcript_variant
	ENST00000524359.1	n.361-16256T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76047 AN: 151644 Hom.: 20225 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.502 AC: 76135 AN: 151762 Hom.: 20264 Cov.: 33 AF XY: 0.496 AC XY: 36820 AN XY: 74164

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.507

Alfa AF: 0.469 Hom.: 10287

Bravo AF: 0.509

Asia WGS AF: 0.338 AC: 1168 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.81
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10105219; hg19: chr8-83857175;