rs17109512

chr10-98367794-G-A

Variant summary

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

The XR_001747305.2(LOC105378449):n.396-401G>A 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 0.0944 in 151,986 control chromosomes in the GnomAD database, including 1,026 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 0.094 (1026 hom., cov: 32)
• Consequence: LOC105378449 XR_001747305.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

LOC105378449 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378449	XR_001747305.2	n.396-401G>A		intron_variant, non_coding_transcript_variant
LOC105378449	XR_946233.3	n.326-401G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14327 AN: 151868 Hom.: 1023 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0944 AC: 14346 AN: 151986 Hom.: 1026 Cov.: 32 AF XY: 0.0971 AC XY: 7214 AN XY: 74286

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.0734

Gnomad4 NFE AF: 0.0347

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0489 Hom.: 608

Bravo AF: 0.106

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.2
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17109512; hg19: chr10-100127551;