4-124417451-G-C

Variant names:

• chr4-124417451-G-C
• rs10518433
• XR_001741822.2:n.77+2811C>G

Variant summary

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

The XR_001741822.2(LOC105377408):​n.77+2811C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,882 control chromosomes in the GnomAD database, including 7,407 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 0.31 (7407 hom., cov: 32)
• Consequence: LOC105377408 XR_001741822.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 1 publications found

Genes affected

LOC105377408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 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: 0.306 AC: 46452 AN: 151764 Hom.: 7406 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.306 AC: 46491 AN: 151882 Hom.: 7407 Cov.: 32 AF XY: 0.307 AC XY: 22760 AN XY: 74186

African (AFR) AF: 0.234 AC: 9712 AN: 41478

American (AMR) AF: 0.332 AC: 5042 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1374 AN: 5144

South Asian (SAS) AF: 0.206 AC: 993 AN: 4814

European-Finnish (FIN) AF: 0.389 AC: 4106 AN: 10548

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22587 AN: 67906

Other (OTH) AF: 0.341 AC: 719 AN: 2110

Alfa AF: 0.204 Hom.: 450

Bravo AF: 0.301

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.55
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs10518433; hg19: chr4-125338606;