rs17042688

chr2-52284656-G-T

Variant summary

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

The NR_135237.1(LOC730100):n.880-31576G>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 0.0821 in 152,204 control chromosomes in the GnomAD database, including 915 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 0.082 (915 hom., cov: 32)
• Consequence: LOC730100 NR_135237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC730100	NR_135237.1	n.880-31576G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440698.1	n.880-31576G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12465 AN: 152086 Hom.: 914 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0831

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0821 AC: 12499 AN: 152204 Hom.: 915 Cov.: 32 AF XY: 0.0824 AC XY: 6134 AN XY: 74408

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0834

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0649

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0426 Hom.: 125

Bravo AF: 0.0897

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.2
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17042688; hg19: chr2-52511794;