rs641025

Positions:

• chr3-152182436-C-G

Variant summary

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

The NR_136178.1(LOC101928166):​n.58-7563G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,944 control chromosomes in the GnomAD database, including 35,914 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 0.68 (35914 hom., cov: 31)
• Consequence: LOC101928166 NR_136178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

ENSG00000289315 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928166	NR_136178.1	n.58-7563G>C		intron_variant
LINC02917	NR_186000.1	n.55+22937G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289315	ENST00000689682.1	n.90-7563G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103941 AN: 151826 Hom.: 35890 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.685 AC: 104026 AN: 151944 Hom.: 35914 Cov.: 31 AF XY: 0.687 AC XY: 51043 AN XY: 74276

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.673

Alfa AF: 0.656 Hom.: 4130

Bravo AF: 0.689

Asia WGS AF: 0.754 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs641025; hg19: chr3-151900225;