rs11880212

chr19-383057-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007067071.1(LOC124904606):n.472T>A 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 0.39 in 152,010 control chromosomes in the GnomAD database, including 12,794 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 0.39 (12794 hom., cov: 32)
• Consequence: LOC124904606 XR_007067071.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

LOC124904606 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904606	XR_007067071.1	n.472T>A		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662087.1	n.96+237T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59145 AN: 151890 Hom.: 12755 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.390 AC: 59240 AN: 152010 Hom.: 12794 Cov.: 32 AF XY: 0.389 AC XY: 28939 AN XY: 74306

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.353

Alfa AF: 0.374 Hom.: 1421

Bravo AF: 0.393

Asia WGS AF: 0.288 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.5
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11880212; hg19: chr19-383057;