chr4-114719413-A-G

Variant names:

• chr4-114719413-A-G
• rs12108602
• XR_007058238.1:n.221-1617T>C

Variant summary

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

The XR_007058238.1(LOC124900763):​n.221-1617T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,112 control chromosomes in the GnomAD database, including 2,690 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 0.18 (2690 hom., cov: 32)
• Consequence: LOC124900763 XR_007058238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.181 AC: 27536 AN: 151994 Hom.: 2684 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.181 AC: 27582 AN: 152112 Hom.: 2690 Cov.: 32 AF XY: 0.183 AC XY: 13574 AN XY: 74348

African (AFR) AF: 0.188 AC: 7785 AN: 41508

American (AMR) AF: 0.203 AC: 3098 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1296 AN: 5170

South Asian (SAS) AF: 0.137 AC: 659 AN: 4822

European-Finnish (FIN) AF: 0.209 AC: 2208 AN: 10586

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11594 AN: 67970

Other (OTH) AF: 0.168 AC: 354 AN: 2112

Alfa AF: 0.172 Hom.: 2303

Bravo AF: 0.183

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.70
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12108602; hg19: chr4-115640569;