rs17503512

Positions:

• chr16-26346113-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_950947.1(LOC102723536):​n.560-17877G>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 0.373 in 152,102 control chromosomes in the GnomAD database, including 10,939 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 0.37 (10939 hom., cov: 32)
• Consequence: LOC102723536 XR_950947.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

Genes affected

LOC102723536 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723536	XR_950947.1	n.560-17877G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56768 AN: 151984 Hom.: 10939 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.373 AC: 56790 AN: 152102 Hom.: 10939 Cov.: 32 AF XY: 0.369 AC XY: 27460 AN XY: 74358

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.394

Alfa AF: 0.377 Hom.: 1859

Bravo AF: 0.379

Asia WGS AF: 0.256 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	1.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17503512; hg19: chr16-26357434;