5-159357103-C-G

Variant summary

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

The NR_037889.1(LOC285626):n.953+2982C>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 0.889 in 152,232 control chromosomes in the GnomAD database, including 60,406 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 0.89 (60406 hom., cov: 31)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

LOC285626 (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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285626	NR_037889.1	n.953+2982C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515337.1	n.953+2982C>G		intron_variant, non_coding_transcript_variant		2
	ENST00000635333.1	n.282+2982C>G		intron_variant, non_coding_transcript_variant		5
	ENST00000641150.1	n.532+2982C>G		intron_variant, non_coding_transcript_variant
	ENST00000648969.1	n.53+2982C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135195 AN: 152114 Hom.: 60342 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.889 AC: 135319 AN: 152232 Hom.: 60406 Cov.: 31 AF XY: 0.892 AC XY: 66388 AN XY: 74430

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.888

Alfa AF: 0.863 Hom.: 7075

Bravo AF: 0.897

Asia WGS AF: 0.955 AC: 3321 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	0.78
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363670; hg19: chr5-158784111;