rs730547

chr17-34785087-C-T

Variant summary

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

The XR_001752848.3(LOC105371742):n.351-22730G>A variant causes a intron, non coding transcript 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_001752848.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

Genes affected

LOC105371742 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105371742	XR_001752848.3	n.351-22730G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0766

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.211

Alfa AF: 0.258 Hom.: 7076

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730547; hg19: chr17-33112106;