XR_007058465.1:n.6304C>T

Variant names:

• chr4-89687808-C-T
• rs3857048
• XR_007058465.1:n.6304C>T

Variant summary

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

The XR_007058465.1(LOC124900602):​n.6304C>T 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 0.26 in 152,126 control chromosomes in the GnomAD database, including 9,036 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 0.26 (9036 hom., cov: 33)
• Consequence: LOC124900602 XR_007058465.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900602	XR_007058465.1	n.6304C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124900602	XR_007058466.1	n.6304C>T		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124900602	XR_001741764.2	n.5498+806C>T		intron_variant	Intron 1 of 2
LOC124900602	XR_938983.2	n.5498+806C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000506864.5	n.472-3477C>T		intron_variant	Intron 3 of 3	4
ENSG00000251095	ENST00000507916.6	n.135-3477C>T		intron_variant	Intron 1 of 2	3
ENSG00000251095	ENST00000508021.5	n.327-3477C>T		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39457 AN: 152008 Hom.: 9007 Cov.: 33

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.260 AC: 39534 AN: 152126 Hom.: 9036 Cov.: 33 AF XY: 0.255 AC XY: 18936 AN XY: 74358

African (AFR) AF: 0.624 AC: 25882 AN: 41482

American (AMR) AF: 0.134 AC: 2044 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.0675 AC: 349 AN: 5172

South Asian (SAS) AF: 0.103 AC: 498 AN: 4820

European-Finnish (FIN) AF: 0.125 AC: 1320 AN: 10576

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8184 AN: 68000

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.163 Hom.: 3367

Bravo AF: 0.275

Asia WGS AF: 0.135 AC: 469 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	2.2
DANN	Benign	0.53
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs3857048; hg19: chr4-90608959;