4-109806404-T-G

Variant names:

• chr4-109806404-T-G
• rs4698790
• XR_007058226.1:n.165-37T>G

Variant summary

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

The XR_007058226.1(LOC124900757):​n.165-37T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,042 control chromosomes in the GnomAD database, including 28,938 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 0.61 (28938 hom., cov: 31)
• Consequence: LOC124900757 XR_007058226.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 11 publications found

Genes affected

LOC124900757 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92326 AN: 151924 Hom.: 28937 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.607 AC: 92365 AN: 152042 Hom.: 28938 Cov.: 31 AF XY: 0.605 AC XY: 44999 AN XY: 74326

African (AFR) AF: 0.458 AC: 19001 AN: 41442

American (AMR) AF: 0.554 AC: 8453 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2227 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3012 AN: 5182

South Asian (SAS) AF: 0.621 AC: 2994 AN: 4820

European-Finnish (FIN) AF: 0.658 AC: 6950 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47770 AN: 67976

Other (OTH) AF: 0.610 AC: 1290 AN: 2114

Alfa AF: 0.668 Hom.: 133839

Bravo AF: 0.589

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.72
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs4698790; hg19: chr4-110727560;