rs7902947

chr10-89825321-T-C

Variant summary

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

The XR_946196.3(LOC105378424):n.792A>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 0.0712 in 152,246 control chromosomes in the GnomAD database, including 840 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 0.071 (840 hom., cov: 33)
• Consequence: LOC105378424 XR_946196.3 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.945

Genes affected

LOC105378424 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378424	XR_946196.3	n.792A>G		splice_region_variant, non_coding_transcript_exon_variant	2/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10810 AN: 152126 Hom.: 831 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0712 AC: 10844 AN: 152246 Hom.: 840 Cov.: 33 AF XY: 0.0726 AC XY: 5405 AN XY: 74454

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.0187

Gnomad4 NFE AF: 0.0111

Gnomad4 OTH AF: 0.0647

Alfa AF: 0.0441 Hom.: 61

Bravo AF: 0.0846

Asia WGS AF: 0.0960 AC: 336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.5
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902947; hg19: chr10-91585078;