rs25531

Positions:

• chr17-30237328-T-C
• chr17-30237328-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The XR_001752824.2(LOC105371720):​n.280+258T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.19 (468 hom., cov: 4)
• Consequence: LOC105371720 XR_001752824.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732

Genes affected

LOC105371720 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BP6: Variant 17-30237328-T-C is Benign according to our data. Variant chr17-30237328-T-C is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371720	XR_001752824.2	n.280+258T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.187 AC: 5881 AN: 31434 Hom.: 464 Cov.: 4

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0938

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.187 AC: 5896 AN: 31456 Hom.: 468 Cov.: 4 AF XY: 0.196 AC XY: 2750 AN XY: 13996

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.186

Alfa AF: 0.0264 Hom.: 20

Bravo AF: 0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs25531; hg19: chr17-28564346;