rs9835451

Variant names:

• chr3-34930072-G-A
• rs9835451
• NR_110817.1:n.207-50606C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-34930072-G-A
• chr3-34930072-G-C
• chr3-34930072-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110817.1(LOC101928135):​n.207-50606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,020 control chromosomes in the GnomAD database, including 60,579 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 0.89 (60579 hom., cov: 30)
• Consequence: LOC101928135 NR_110817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

Genes affected

LOC101928135 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928135	NR_110817.1	n.207-50606C>T		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135461 AN: 151904 Hom.: 60532 Cov.: 30

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.892 AC: 135561 AN: 152020 Hom.: 60579 Cov.: 30 AF XY: 0.889 AC XY: 66050 AN XY: 74284

African (AFR) AF: 0.933 AC: 38702 AN: 41490

American (AMR) AF: 0.887 AC: 13544 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3194 AN: 3468

East Asian (EAS) AF: 0.825 AC: 4246 AN: 5144

South Asian (SAS) AF: 0.845 AC: 4068 AN: 4816

European-Finnish (FIN) AF: 0.848 AC: 8959 AN: 10568

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59857 AN: 67956

Other (OTH) AF: 0.894 AC: 1882 AN: 2106

Alfa AF: 0.885 Hom.: 11493

Bravo AF: 0.896

Asia WGS AF: 0.835 AC: 2905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.029
DANN	Benign	0.21
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9835451; hg19: chr3-34971564;