rs7918018

Positions:

• chr10-89825521-C-G

Variant summary

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

The XR_946196.3(LOC105378424):​n.791-199G>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 0.26 in 152,064 control chromosomes in the GnomAD database, including 6,684 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 0.26 (6684 hom., cov: 33)
• Consequence: LOC105378424 XR_946196.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

LOC105378424 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378424	XR_946196.3	n.791-199G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39437 AN: 151946 Hom.: 6647 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.260 AC: 39528 AN: 152064 Hom.: 6684 Cov.: 33 AF XY: 0.265 AC XY: 19707 AN XY: 74328

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.244

Alfa AF: 0.208 Hom.: 559

Bravo AF: 0.267

Asia WGS AF: 0.346 AC: 1202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7918018; hg19: chr10-91585278;