rs17634917

chr19-55754298-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105372465 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 114 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372465	XR_936081.2	n.226A>G		non_coding_transcript_exon_variant	2/3

Ensembl

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

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

Gnomad4 AFR AF: 0.00895

Gnomad4 AMR AF: 0.0306

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00912

Gnomad4 FIN AF: 0.0605

Gnomad4 NFE AF: 0.0483

Gnomad4 OTH AF: 0.0274

Alfa AF: 0.0381 Hom.: 33

Bravo AF: 0.0312

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.37
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17634917; hg19: chr19-56265664;