rs17691914

chr3-34921311-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.207-41845T>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 0.0628 in 152,298 control chromosomes in the GnomAD database, including 428 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 0.063 (428 hom., cov: 33)
• Consequence: LOC101928135 NR_110817.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928135	NR_110817.1	n.207-41845T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0628 AC: 9555 AN: 152180 Hom.: 424 Cov.: 33

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0790

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0628 AC: 9568 AN: 152298 Hom.: 428 Cov.: 33 AF XY: 0.0643 AC XY: 4788 AN XY: 74474

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.0874

Gnomad4 NFE AF: 0.0790

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0774 Hom.: 78

Bravo AF: 0.0604

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.8
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17691914; hg19: chr3-34962803;