rs1118997

chr14-44520496-C-T

Variant summary

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

The NR_135257.1(LOC105370473):n.139+11767C>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 0.189 in 151,980 control chromosomes in the GnomAD database, including 3,381 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 0.19 (3381 hom., cov: 32)
• Consequence: LOC105370473 NR_135257.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370473	NR_135257.1	n.139+11767C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662197.1	n.163+11767C>T		intron_variant, non_coding_transcript_variant
	ENST00000555433.1	n.139+11767C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000556228.1	n.229+11265C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28660 AN: 151862 Hom.: 3366 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.189 AC: 28704 AN: 151980 Hom.: 3381 Cov.: 32 AF XY: 0.194 AC XY: 14426 AN XY: 74312

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.183

Alfa AF: 0.150 Hom.: 271

Bravo AF: 0.205

Asia WGS AF: 0.334 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.3
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1118997; hg19: chr14-44989699;