rs17288584

Positions:

• chr18-71467426-G-A
• chr18-71467426-G-C

Variant summary

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

The XR_001753502.1(LOC107985179):​n.64+35278G>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 0.036 in 152,184 control chromosomes in the GnomAD database, including 157 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 0.036 (157 hom., cov: 32)
• Consequence: LOC107985179 XR_001753502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.268

Genes affected

LOC107985179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985179	XR_001753502.1	n.64+35278G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5478 AN: 152068 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.00845

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0573

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0360 AC: 5475 AN: 152184 Hom.: 157 Cov.: 32 AF XY: 0.0350 AC XY: 2604 AN XY: 74390

Gnomad4 AFR AF: 0.00843

Gnomad4 AMR AF: 0.0194

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.0269

Alfa AF: 0.0466 Hom.: 36

Bravo AF: 0.0318

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
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: rs17288584; hg19: chr18-69134662;