XR_001752843.3:n.354-22730G>A

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_001752843.3(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_001752843.3 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371742	XR_001752843.3	n.354-22730G>A		intron_variant	Intron 3 of 3
LOC105371742	XR_001752844.3	n.354-22730G>A		intron_variant	Intron 3 of 4
LOC105371742	XR_001752845.3	n.354-22730G>A		intron_variant	Intron 3 of 4

Ensembl

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

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 v4.3

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

Other links and lift over

dbSNP: rs730547; hg19: chr17-33112106;