rs17583753

Positions:

• chr4-99264507-G-A
• chr4-99264507-G-C
• chr4-99264507-G-T

Variant summary

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

The NR_037884.1(LOC100507053):​n.3790-22288G>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 0.0971 in 152,228 control chromosomes in the GnomAD database, including 990 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 0.097 (990 hom., cov: 32)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3790-22288G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000500358.6	n.3790-22288G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14783 AN: 152110 Hom.: 990 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0971 AC: 14786 AN: 152228 Hom.: 990 Cov.: 32 AF XY: 0.0956 AC XY: 7113 AN XY: 74398

Gnomad4 AFR AF: 0.0229

Gnomad4 AMR AF: 0.0965

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0359

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0984 Hom.: 289

Bravo AF: 0.0900

Asia WGS AF: 0.0260 AC: 93 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	1.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17583753; hg19: chr4-100185664;