3-35346652-C-T

Variant summary

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

The NR_110817.1(LOC101928135):n.153-40128G>A 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 0.216 in 151,372 control chromosomes in the GnomAD database, including 6,416 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 0.22 (6416 hom., cov: 32)
• Consequence: LOC101928135 NR_110817.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928135	NR_110817.1	n.153-40128G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32708 AN: 151254 Hom.: 6413 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.216 AC: 32741 AN: 151372 Hom.: 6416 Cov.: 32 AF XY: 0.211 AC XY: 15609 AN XY: 73960

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0595

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.216

Alfa AF: 0.0758 Hom.: 172

Bravo AF: 0.236

Asia WGS AF: 0.135 AC: 469 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.011
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160578; hg19: chr3-35388144;