XR_001740993.2:n.10928+3300C>T

Variant names:

• chr3-161275076-C-T
• rs34016896
• XR_001740993.2:n.10928+3300C>T

Variant summary

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

The XR_001740993.2(LOC105374187):​n.10928+3300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,036 control chromosomes in the GnomAD database, including 6,813 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 0.29 (6813 hom., cov: 33)
• Consequence: LOC105374187 XR_001740993.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 22 publications found

Genes affected

LOC105374187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43401 AN: 151918 Hom.: 6811 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.286 AC: 43413 AN: 152036 Hom.: 6813 Cov.: 33 AF XY: 0.290 AC XY: 21521 AN XY: 74304

African (AFR) AF: 0.165 AC: 6832 AN: 41472

American (AMR) AF: 0.364 AC: 5564 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2745 AN: 5172

South Asian (SAS) AF: 0.355 AC: 1706 AN: 4810

European-Finnish (FIN) AF: 0.311 AC: 3283 AN: 10548

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21196 AN: 67976

Other (OTH) AF: 0.279 AC: 589 AN: 2112

Alfa AF: 0.312 Hom.: 2144

Bravo AF: 0.283

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs34016896; hg19: chr3-160992864;