rs360719

Variant names:

• chr11-112165426-A-G
• rs360719
• ENST00000532699.1:n.315-4993A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532699.1(ENSG00000255292):​n.315-4993A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,150 control chromosomes in the GnomAD database, including 5,024 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 0.25 (5024 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 48 publications found

Genes affected

ENSG00000255292 (HGNC:):

ENSG00000254638 (HGNC:58436):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX12-AS1	XR_001748384.2	n.276T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255292	ENST00000532699.1	n.315-4993A>G		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000254638	ENST00000527589.1	n.365T>C		non_coding_transcript_exon_variant	Exon 4 of 4	3
ENSG00000255292	ENST00000525987.5	n.320-4993A>G		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.315-4993A>G		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38321 AN: 152030 Hom.: 5025 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.252 AC: 38313 AN: 152148 Hom.: 5024 Cov.: 33 AF XY: 0.252 AC XY: 18757 AN XY: 74388

African (AFR) AF: 0.209 AC: 8695 AN: 41518

American (AMR) AF: 0.302 AC: 4619 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3464

East Asian (EAS) AF: 0.128 AC: 663 AN: 5188

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4824

European-Finnish (FIN) AF: 0.287 AC: 3037 AN: 10586

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18512 AN: 67964

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.250 Hom.: 695

Bravo AF: 0.253

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.71
PhyloP100		-0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs360719; hg19: chr11-112036149;