rs17634917

Variant names:

• chr19-55754298-A-G
• rs17634917
• XR_936081.2:n.226A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_936081.2(LOC105372465):​n.226A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.033 in 152,304 control chromosomes in the GnomAD database, including 114 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 0.033 (114 hom., cov: 32)
• Consequence: LOC105372465 XR_936081.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 8 publications found

Genes affected

LOC105372465 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.033 (5021/152304) while in subpopulation NFE AF = 0.0483 (3285/68022). AF 95% confidence interval is 0.0469. There are 114 homozygotes in GnomAd4. There are 2409 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 114 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0330 AC: 5025 AN: 152186 Hom.: 114 Cov.: 32

Gnomad AFR AF: 0.00897

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0330 AC: 5021 AN: 152304 Hom.: 114 Cov.: 32 AF XY: 0.0323 AC XY: 2409 AN XY: 74470

African (AFR) AF: 0.00895 AC: 372 AN: 41572

American (AMR) AF: 0.0306 AC: 468 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00912 AC: 44 AN: 4824

European-Finnish (FIN) AF: 0.0605 AC: 642 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0483 AC: 3285 AN: 68022

Other (OTH) AF: 0.0274 AC: 58 AN: 2114

Alfa AF: 0.0318 Hom.: 75

Bravo AF: 0.0312

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.59
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs17634917; hg19: chr19-56265664;