rs12459897

Positions:

• chr19-31105872-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000638312.1(ENSG00000284430):​n.191+5378G>T 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 0.0123 in 152,282 control chromosomes in the GnomAD database, including 23 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 0.012 (23 hom., cov: 32)
• Consequence: ENST00000638312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0123 (1868/152282) while in subpopulation NFE AF= 0.0179 (1220/68028). AF 95% confidence interval is 0.0171. There are 23 homozygotes in gnomad4. There are 844 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 23 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900621	XR_935901.2	n.51+5378G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000638312.1	n.191+5378G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0123 AC: 1866 AN: 152164 Hom.: 23 Cov.: 32

Gnomad AFR AF: 0.00275

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.00864

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00332

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0179

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0123 AC: 1868 AN: 152282 Hom.: 23 Cov.: 32 AF XY: 0.0113 AC XY: 844 AN XY: 74462

Gnomad4 AFR AF: 0.00274

Gnomad4 AMR AF: 0.00863

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00353

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.0179

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.0134 Hom.: 2

Bravo AF: 0.0119

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12459897; hg19: chr19-31596778;