rs2602836

chr4-99093654-A-G

Variant summary

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

The NR_037884.1(LOC100507053):n.428+4370A>G 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 0.509 in 152,074 control chromosomes in the GnomAD database, including 21,086 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 0.51 (21086 hom., cov: 33)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.428+4370A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.428+4370A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77355 AN: 151954 Hom.: 21083 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.509 AC: 77373 AN: 152074 Hom.: 21086 Cov.: 33 AF XY: 0.515 AC XY: 38260 AN XY: 74324

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.526

Alfa AF: 0.570 Hom.: 57707

Bravo AF: 0.488

Asia WGS AF: 0.749 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.8
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2602836; hg19: chr4-100014805;