rs6505172

Positions:

• chr17-30311826-T-C

Variant summary

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

The XR_934656.2(LOC105371721):​n.86-779A>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 0.103 in 152,094 control chromosomes in the GnomAD database, including 1,489 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 0.10 (1489 hom., cov: 31)
• Consequence: LOC105371721 XR_934656.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

Genes affected

LOC105371721 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371721	XR_934656.2	n.86-779A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15689 AN: 151976 Hom.: 1485 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.103 AC: 15711 AN: 152094 Hom.: 1489 Cov.: 31 AF XY: 0.102 AC XY: 7621 AN XY: 74370

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.0586

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.0443

Gnomad4 SAS AF: 0.0956

Gnomad4 FIN AF: 0.0411

Gnomad4 NFE AF: 0.0439

Gnomad4 OTH AF: 0.0948

Alfa AF: 0.0790 Hom.: 106

Bravo AF: 0.110

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6505172; hg19: chr17-28638844;