rs10499068

chr6-112761302-A-G

Variant summary

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

The XR_001744301.2(LOC107986634):n.60-29367T>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 0.1 in 152,160 control chromosomes in the GnomAD database, including 978 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 0.10 (978 hom., cov: 32)
• Consequence: LOC107986634 XR_001744301.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

Genes affected

LOC107986634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986634	XR_001744301.2	n.60-29367T>C		intron_variant, non_coding_transcript_variant
LOC105377949	XR_001744304.2	n.645-8430A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15239 AN: 152042 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.100 AC: 15239 AN: 152160 Hom.: 978 Cov.: 32 AF XY: 0.101 AC XY: 7545 AN XY: 74390

Gnomad4 AFR AF: 0.0214

Gnomad4 AMR AF: 0.0859

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.108

Alfa AF: 0.119 Hom.: 162

Bravo AF: 0.0908

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	11
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499068; hg19: chr6-113082504;