XR_007058238.1:n.293+279C>G

Variant names:

• chr4-114717445-G-C
• rs78557978
• XR_007058238.1:n.293+279C>G

Variant summary

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

The XR_007058238.1(LOC124900763):​n.293+279C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.035 in 151,896 control chromosomes in the GnomAD database, including 517 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 0.035 (517 hom., cov: 32)
• Consequence: LOC124900763 XR_007058238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 4 publications found

Genes affected

LOC124900763 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0351 AC: 5329 AN: 151774 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.00550

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0233

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00767

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0350 AC: 5317 AN: 151896 Hom.: 517 Cov.: 32 AF XY: 0.0434 AC XY: 3220 AN XY: 74218

African (AFR) AF: 0.00548 AC: 227 AN: 41428

American (AMR) AF: 0.0671 AC: 1024 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0233 AC: 81 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1854 AN: 5164

South Asian (SAS) AF: 0.184 AC: 886 AN: 4812

European-Finnish (FIN) AF: 0.0610 AC: 641 AN: 10514

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00767 AC: 521 AN: 67936

Other (OTH) AF: 0.0242 AC: 51 AN: 2104

Alfa AF: 0.00367 Hom.: 0

Bravo AF: 0.0318

Asia WGS AF: 0.227 AC: 786 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs78557978; hg19: chr4-115638601;