4-89681893-A-G

Variant names:

• chr4-89681893-A-G
• rs17015982
• XR_001741764.2:n.389A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741764.2(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_001741764.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 2 publications found

Genes affected

LOC124900602 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124900602	XR_001741764.2	n.389A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124900602	XR_007058465.1	n.389A>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124900602	XR_007058466.1	n.389A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124900602	XR_938983.2	n.389A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000506864.5	n.472-9392A>G		intron_variant	Intron 3 of 3	4
ENSG00000251095	ENST00000507916.6	n.135-9392A>G		intron_variant	Intron 1 of 2	3
ENSG00000251095	ENST00000508021.5	n.327-9392A>G		intron_variant	Intron 3 of 4	4

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

African (AFR) AF: 0.403 AC: 16707 AN: 41412

American (AMR) AF: 0.0843 AC: 1289 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.0555 AC: 288 AN: 5188

South Asian (SAS) AF: 0.0876 AC: 422 AN: 4818

European-Finnish (FIN) AF: 0.102 AC: 1076 AN: 10552

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5087 AN: 67998

Other (OTH) AF: 0.142 AC: 299 AN: 2112

Alfa AF: 0.0949 Hom.: 851

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
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs17015982; hg19: chr4-90603044;