rs17015982

Positions:

• chr4-89681893-A-G

Variant summary

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

The XR_007058466.1(LOC124900602):​n.389A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,050 control chromosomes in the GnomAD database, including 3,847 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 0.17 (3847 hom., cov: 33)
• Consequence: LOC124900602 XR_007058466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

Genes affected

LOC124900602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900602	XR_007058466.1	n.389A>G		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_001741764.2	n.389A>G		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_007058465.1	n.389A>G		non_coding_transcript_exon_variant	1/2
LOC124900602	XR_938983.2	n.389A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659878.1	n.480-44491A>G		intron_variant, non_coding_transcript_variant
	ENST00000673949.1	n.305+20381T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25492 AN: 151932 Hom.: 3829 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.168 AC: 25547 AN: 152050 Hom.: 3847 Cov.: 33 AF XY: 0.166 AC XY: 12368 AN XY: 74318

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.0876

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0930 Hom.: 735

Bravo AF: 0.176

Asia WGS AF: 0.105 AC: 364 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17015982; hg19: chr4-90603044;