rs10487488

chr7-127509237-A-C

Variant summary

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

The XR_007060511.1(LOC105375490):n.176T>G 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 0.105 in 152,230 control chromosomes in the GnomAD database, including 892 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 0.11 (892 hom., cov: 32)
• Consequence: LOC105375490 XR_007060511.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375490	XR_007060511.1	n.176T>G		splice_region_variant, non_coding_transcript_exon_variant	3/5
LOC105375490	XR_001745351.2	n.2293T>G		splice_region_variant, non_coding_transcript_exon_variant	3/5
LOC105375490	XR_001745352.2	n.495T>G		splice_region_variant, non_coding_transcript_exon_variant	4/6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16025 AN: 152112 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0935

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.105 AC: 16030 AN: 152230 Hom.: 892 Cov.: 32 AF XY: 0.106 AC XY: 7864 AN XY: 74444

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0820

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.0931

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0953

Alfa AF: 0.0976 Hom.: 455

Bravo AF: 0.103

Asia WGS AF: 0.0950 AC: 333 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	18
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487488; hg19: chr7-127149291;