rs10499299

Positions:

• chr6-155812754-A-G

Variant summary

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

The XR_001744423.2(LOC101928923):​n.699-715T>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 0.135 in 152,130 control chromosomes in the GnomAD database, including 1,509 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 0.14 (1509 hom., cov: 32)
• Consequence: LOC101928923 XR_001744423.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

LOC101928923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928923	XR_001744423.2	n.699-715T>C		intron_variant, non_coding_transcript_variant
LOC105378072	XR_001744424.2	n.79+19335A>G		intron_variant, non_coding_transcript_variant
LOC105378072	XR_007059824.1	n.79+19335A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20514 AN: 152012 Hom.: 1500 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.135 AC: 20554 AN: 152130 Hom.: 1509 Cov.: 32 AF XY: 0.134 AC XY: 9960 AN XY: 74372

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0562

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.125

Alfa AF: 0.133 Hom.: 1851

Bravo AF: 0.139

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499299; hg19: chr6-156133888;