4-165359528-T-C

Variant names:

• chr4-165359528-T-C
• rs4690810
• XR_939416.2:n.570-1562T>C

Variant summary

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

The XR_939416.2(LOC105377519):​n.570-1562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,008 control chromosomes in the GnomAD database, including 10,609 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 0.37 (10609 hom., cov: 33)
• Consequence: LOC105377519 XR_939416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 2 publications found

Genes affected

LOC105377519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 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: 0.370 AC: 56153 AN: 151890 Hom.: 10612 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.369 AC: 56165 AN: 152008 Hom.: 10609 Cov.: 33 AF XY: 0.367 AC XY: 27251 AN XY: 74280

African (AFR) AF: 0.379 AC: 15706 AN: 41454

American (AMR) AF: 0.326 AC: 4989 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2965 AN: 5172

South Asian (SAS) AF: 0.444 AC: 2142 AN: 4824

European-Finnish (FIN) AF: 0.342 AC: 3605 AN: 10546

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24231 AN: 67946

Other (OTH) AF: 0.377 AC: 793 AN: 2106

Alfa AF: 0.237 Hom.: 579

Bravo AF: 0.368

Asia WGS AF: 0.448 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.79
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs4690810; hg19: chr4-166280680;