3-35035517-C-T

Variant names:

• chr3-35035517-C-T
• rs17032625
• NR_110817.1:n.207-156051G>A

Variant summary

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

The NR_110817.1(LOC101928135):​n.207-156051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 151,848 control chromosomes in the GnomAD database, including 618 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 0.078 (618 hom., cov: 30)
• Consequence: LOC101928135 NR_110817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928135	NR_110817.1	n.207-156051G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11822 AN: 151730 Hom.: 620 Cov.: 30

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0780

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0932

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0779 AC: 11823 AN: 151848 Hom.: 618 Cov.: 30 AF XY: 0.0796 AC XY: 5908 AN XY: 74224

Gnomad4 AFR AF: 0.0503

Gnomad4 AMR AF: 0.0620

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0508 Hom.: 49

Bravo AF: 0.0765

Asia WGS AF: 0.140 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17032625; hg19: chr3-35077009;