rs11575981

chr14-20891294-C-T

Variant summary

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

The XR_110261.4(LOC100507513):n.723-15551G>A 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 0.00694 in 216,494 control chromosomes in the GnomAD database, including 44 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 0.0070 (28 hom., cov: 31)
  • Exomes 𝑓: 0.0067 (16 hom.)
• Consequence: LOC100507513 XR_110261.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371

Genes affected

LOC100507513 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507513	XR_110261.4	n.723-15551G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00706 AC: 1066 AN: 151054 Hom.: 28 Cov.: 31

Gnomad AFR AF: 0.00124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00145

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000867

Gnomad OTH AF: 0.00432

GnomAD4 exome AF: 0.00669 AC: 437 AN: 65324 Hom.: 16 AF XY: 0.00623 AC XY: 206 AN XY: 33070

Gnomad4 AFR exome AF: 0.00225

Gnomad4 AMR exome AF: 0.00381

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0724

Gnomad4 SAS exome AF: 0.00222

Gnomad4 FIN exome AF: 0.0301

Gnomad4 NFE exome AF: 0.000746

Gnomad4 OTH exome AF: 0.00462

GnomAD4 genome AF: 0.00705 AC: 1065 AN: 151170 Hom.: 28 Cov.: 31 AF XY: 0.00917 AC XY: 678 AN XY: 73940

Gnomad4 AFR AF: 0.00123

Gnomad4 AMR AF: 0.00144

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.00395

Gnomad4 FIN AF: 0.0336

Gnomad4 NFE AF: 0.000867

Gnomad4 OTH AF: 0.00475

Alfa AF: 0.00353 Hom.: 0

Bravo AF: 0.00488

Asia WGS AF: 0.0530 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	9.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11575981; hg19: chr14-21359453;