rs10487488

Variant names:

• chr7-127509237-A-C
• rs10487488
• XR_001745351.2:n.2293T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745351.2(LOC105375490):​n.2293T>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_001745351.2 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923
• Publications: 7 publications found

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375490	XR_001745351.2	n.2293T>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 5
LOC105375490	XR_001745352.2	n.495T>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 4 of 6
LOC105375490	XR_007060511.1	n.176T>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295686	ENST00000731796.1	n.70-3871T>G		intron_variant	Intron 1 of 2
ENSG00000295686	ENST00000731797.1	n.355-23955T>G		intron_variant	Intron 3 of 3
ENSG00000295686	ENST00000731798.1	n.244-3871T>G		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.124 AC: 5150 AN: 41522

American (AMR) AF: 0.0820 AC: 1253 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3472

East Asian (EAS) AF: 0.0931 AC: 483 AN: 5188

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4824

European-Finnish (FIN) AF: 0.129 AC: 1370 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6838 AN: 68018

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0972 Hom.: 488

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
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs10487488; hg19: chr7-127149291;