17-34785087-C-T

Variant names:

• chr17-34785087-C-T
• rs730547
• XR_001752843.3:n.354-22730G>A

Variant summary

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

The XR_934691.4(LOC105371742):​n.354-22730G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,222 control chromosomes in the GnomAD database, including 3,778 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 0.20 (3778 hom., cov: 33)
• Consequence: LOC105371742 XR_934691.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 10 publications found

Genes affected

LOC105371742 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 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: 0.198 AC: 30184 AN: 152104 Hom.: 3775 Cov.: 33

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.198 AC: 30188 AN: 152222 Hom.: 3778 Cov.: 33 AF XY: 0.196 AC XY: 14596 AN XY: 74426

African (AFR) AF: 0.0520 AC: 2159 AN: 41548

American (AMR) AF: 0.339 AC: 5188 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3470

East Asian (EAS) AF: 0.0766 AC: 397 AN: 5184

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4822

European-Finnish (FIN) AF: 0.189 AC: 2004 AN: 10610

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17583 AN: 67990

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.253 Hom.: 8765

Bravo AF: 0.206

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.79
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs730547;

hg19: chr17-33112106;