rs9896573

Positions:

• chr17-70142903-T-C
• chr17-70142903-T-G

Variant summary

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

The XR_934953.3(LOC105371882):​n.425-4470A>G 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 0.113 in 152,290 control chromosomes in the GnomAD database, including 951 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 0.11 (951 hom., cov: 32)
• Consequence: LOC105371882 XR_934953.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

LOC105371882 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371882	XR_934953.3	n.425-4470A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17261 AN: 152172 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0860

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.113 AC: 17275 AN: 152290 Hom.: 951 Cov.: 32 AF XY: 0.114 AC XY: 8505 AN XY: 74468

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0958

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0766 Hom.: 109

Bravo AF: 0.118

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9896573; hg19: chr17-68139044;