rs10486000

Positions:

• chr7-97515457-C-G

Variant summary

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

The XR_001745293.1(LOC105375416):​n.22-5280G>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 0.0273 in 152,236 control chromosomes in the GnomAD database, including 91 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 0.027 (91 hom., cov: 33)
• Consequence: LOC105375416 XR_001745293.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

LOC105375416 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375416	XR_001745293.1	n.22-5280G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4144 AN: 152118 Hom.: 89 Cov.: 33

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0273 AC: 4163 AN: 152236 Hom.: 91 Cov.: 33 AF XY: 0.0297 AC XY: 2208 AN XY: 74428

Gnomad4 AFR AF: 0.0260

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0498

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0205

Gnomad4 OTH AF: 0.0269

Alfa AF: 0.0234 Hom.: 8

Bravo AF: 0.0266

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486000; hg19: chr7-97144769;