rs13104485

chr4-99219666-T-A

Variant summary

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

The NR_037884.1(LOC100507053):n.3789+15235T>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 0.373 in 153,236 control chromosomes in the GnomAD database, including 12,195 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 0.37 (12050 hom., cov: 32)
  • Exomes 𝑓: 0.45 (145 hom.)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.3789+15235T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.3789+15235T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56617 AN: 151844 Hom.: 12048 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.427

GnomAD4 exome AF: 0.447 AC: 569 AN: 1274 Hom.: 145 AF XY: 0.429 AC XY: 333 AN XY: 776

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.583

Gnomad4 ASJ exome AF: 0.615

Gnomad4 EAS exome AF: 0.219

Gnomad4 SAS exome AF: 0.292

Gnomad4 FIN exome AF: 0.583

Gnomad4 NFE exome AF: 0.453

Gnomad4 OTH exome AF: 0.466

GnomAD4 genome AF: 0.373 AC: 56650 AN: 151962 Hom.: 12050 Cov.: 32 AF XY: 0.371 AC XY: 27540 AN XY: 74272

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.425

Alfa AF: 0.411 Hom.: 1654

Bravo AF: 0.369

Asia WGS AF: 0.222 AC: 775 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.51
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13104485; hg19: chr4-100140823;