chr17-56533930-C-T

Variant names:

• chr17-56533930-C-T
• rs17760268
• XR_002958121.1:n.389-814G>A

Variant summary

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

The XR_002958121.1(LOC112268194):​n.389-814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,316 control chromosomes in the GnomAD database, including 346 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 0.056 (346 hom., cov: 32)
• Consequence: LOC112268194 XR_002958121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

Genes affected

LOC112268194 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268194	XR_002958121.1	n.389-814G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8592 AN: 152198 Hom.: 346 Cov.: 32

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0484

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0564 AC: 8586 AN: 152316 Hom.: 346 Cov.: 32 AF XY: 0.0545 AC XY: 4059 AN XY: 74488

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.0666

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0480

Gnomad4 FIN AF: 0.0365

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0737 Hom.: 239

Bravo AF: 0.0565

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.72
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17760268; hg19: chr17-54611291;