17-69362956-C-T

Variant names:

• chr17-69362956-C-T
• rs560271
• XR_934950.3:n.-27G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_934950.3(LOC105371879):​n.-27G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,200 control chromosomes in the GnomAD database, including 1,126 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 0.11 (1126 hom., cov: 32)
• Consequence: LOC105371879 XR_934950.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 5 publications found

Genes affected

LOC105371879 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371879	XR_934950.3	n.-27G>A		upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16009 AN: 152082 Hom.: 1125 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.105 AC: 16012 AN: 152200 Hom.: 1126 Cov.: 32 AF XY: 0.102 AC XY: 7625 AN XY: 74406

African (AFR) AF: 0.0315 AC: 1310 AN: 41548

American (AMR) AF: 0.106 AC: 1613 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0511 AC: 247 AN: 4830

European-Finnish (FIN) AF: 0.120 AC: 1268 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10818 AN: 67988

Other (OTH) AF: 0.103 AC: 217 AN: 2110

Alfa AF: 0.124 Hom.: 1607

Bravo AF: 0.101

Asia WGS AF: 0.0330 AC: 113 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	6.4
DANN	Benign	0.64
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs560271; hg19: chr17-67359097;