rs10787516

Positions:

• chr10-114054165-C-T

Variant summary

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

The XR_007062383.1(LOC124902554):​n.194-6970G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,064 control chromosomes in the GnomAD database, including 14,925 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 0.41 (14925 hom., cov: 33)
• Consequence: LOC124902554 XR_007062383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

Genes affected

LOC124902554 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902554	XR_007062383.1	n.194-6970G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63061 AN: 151946 Hom.: 14929 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.415 AC: 63064 AN: 152064 Hom.: 14925 Cov.: 33 AF XY: 0.423 AC XY: 31426 AN XY: 74312

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.417

Alfa AF: 0.484 Hom.: 30484

Bravo AF: 0.392

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10787516; hg19: chr10-115813924;