rs10514688

chr3-34921177-T-C

Variant summary

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

The NR_110817.1(LOC101928135):n.207-41711A>G 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 0.116 in 152,268 control chromosomes in the GnomAD database, including 1,124 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 0.12 (1124 hom., cov: 33)
• Consequence: LOC101928135 NR_110817.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928135	NR_110817.1	n.207-41711A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17649 AN: 152150 Hom.: 1118 Cov.: 33

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.0815

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.116 AC: 17672 AN: 152268 Hom.: 1124 Cov.: 33 AF XY: 0.118 AC XY: 8822 AN XY: 74452

Gnomad4 AFR AF: 0.0941

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0798

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.110

Alfa AF: 0.120 Hom.: 1728

Bravo AF: 0.113

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	10
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514688; hg19: chr3-34962669;