chr17-69339641-C-T

Variant names:

• chr17-69339641-C-T
• rs558076
• XR_934949.2:n.187-3659C>T

Variant summary

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

The XR_934949.2(LOC105371878):​n.187-3659C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,038 control chromosomes in the GnomAD database, including 5,110 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 0.25 (5110 hom., cov: 32)
• Consequence: LOC105371878 XR_934949.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943
• Publications: 6 publications found

Genes affected

LOC105371878 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38266 AN: 151920 Hom.: 5096 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.252 AC: 38299 AN: 152038 Hom.: 5110 Cov.: 32 AF XY: 0.256 AC XY: 19001 AN XY: 74334

African (AFR) AF: 0.160 AC: 6638 AN: 41504

American (AMR) AF: 0.269 AC: 4109 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1969 AN: 5162

South Asian (SAS) AF: 0.305 AC: 1472 AN: 4824

European-Finnish (FIN) AF: 0.304 AC: 3207 AN: 10554

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19380 AN: 67930

Other (OTH) AF: 0.276 AC: 583 AN: 2114

Alfa AF: 0.272 Hom.: 25705

Bravo AF: 0.246

Asia WGS AF: 0.322 AC: 1116 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.24
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs558076; hg19: chr17-67335782;