rs17075980

Positions:

• chr5-173465325-C-T

Variant summary

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

The XR_001743001.1(LOC105377732):​n.524-4144C>T 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 0.297 in 152,126 control chromosomes in the GnomAD database, including 8,703 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 0.30 (8703 hom., cov: 33)
• Consequence: LOC105377732 XR_001743001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

LOC105377732 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377732	XR_001743001.1	n.524-4144C>T		intron_variant, non_coding_transcript_variant
LOC105377732	XR_007059057.1	n.1488+1386C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000519400.2	n.261+1581C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000662094.1	n.432+1386C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45068 AN: 152006 Hom.: 8674 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.297 AC: 45146 AN: 152126 Hom.: 8703 Cov.: 33 AF XY: 0.291 AC XY: 21658 AN XY: 74372

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0942

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.250

Alfa AF: 0.215 Hom.: 5431

Bravo AF: 0.305

Asia WGS AF: 0.116 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.026
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17075980; hg19: chr5-172892328;