rs10484554

chr6-31306778-C-T

Variant summary

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

The XR_926691.3(LOC112267902):n.964G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,892 control chromosomes in the GnomAD database, including 1,330 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 0.12 (1330 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.964G>A		splice_region_variant, non_coding_transcript_exon_variant	3/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18814 AN: 151774 Hom.: 1330 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0517

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.124 AC: 18817 AN: 151892 Hom.: 1330 Cov.: 32 AF XY: 0.124 AC XY: 9221 AN XY: 74244

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0520

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.134

Alfa AF: 0.143 Hom.: 2975

Bravo AF: 0.124

Asia WGS AF: 0.0930 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484554; hg19: chr6-31274555;