rs13123099

chr4-99273360-G-A

Variant summary

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

The NR_037884.1(LOC100507053):n.3790-13435G>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 0.275 in 152,098 control chromosomes in the GnomAD database, including 7,056 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 0.27 (7056 hom., cov: 32)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.3790-13435G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.3790-13435G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41751 AN: 151980 Hom.: 7060 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.275 AC: 41752 AN: 152098 Hom.: 7056 Cov.: 32 AF XY: 0.268 AC XY: 19924 AN XY: 74354

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.0262

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.328

Alfa AF: 0.362 Hom.: 10332

Bravo AF: 0.261

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.41
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13123099; hg19: chr4-100194517;