rs117020818

Positions:

• chr11-13107616-G-A
• chr11-13107616-G-T

Variant summary

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

The ENST00000531136.1(ENSG00000255558):​n.47+27177C>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 0.0217 in 152,044 control chromosomes in the GnomAD database, including 55 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 0.022 (55 hom., cov: 32)
• Consequence: ENST00000531136.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0217 (3295/152044) while in subpopulation AMR AF= 0.0393 (600/15260). AF 95% confidence interval is 0.0367. There are 55 homozygotes in gnomad4. There are 1567 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 55 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000531136.1	n.47+27177C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0217 AC: 3293 AN: 151926 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.00583

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00520

Gnomad FIN AF: 0.0152

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0321

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0217 AC: 3295 AN: 152044 Hom.: 55 Cov.: 32 AF XY: 0.0211 AC XY: 1567 AN XY: 74332

Gnomad4 AFR AF: 0.00581

Gnomad4 AMR AF: 0.0393

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00521

Gnomad4 FIN AF: 0.0152

Gnomad4 NFE AF: 0.0321

Gnomad4 OTH AF: 0.0209

Alfa AF: 0.0181 Hom.: 11

Bravo AF: 0.0224

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117020818; hg19: chr11-13129163;