3-35346896-A-G

Position:

• chr3-35346896-A-G

Variant summary

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

The NR_110817.1(LOC101928135):​n.153-40372T>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 0.133 in 151,350 control chromosomes in the GnomAD database, including 1,867 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 0.13 (1867 hom., cov: 32)
• Consequence: LOC101928135 NR_110817.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928135	NR_110817.1	n.153-40372T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20054 AN: 151232 Hom.: 1870 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.0840

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.133 AC: 20072 AN: 151350 Hom.: 1867 Cov.: 32 AF XY: 0.128 AC XY: 9488 AN XY: 73980

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0391

Gnomad4 NFE AF: 0.0840

Gnomad4 OTH AF: 0.149

Alfa AF: 0.106 Hom.: 204

Bravo AF: 0.144

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7631209; hg19: chr3-35388388;