rs1442855

Variant names:

• chr4-43321899-C-T
• rs1442855
• XR_925266.3:n.202+5618C>T

Variant summary

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

The XR_925266.3(LOC105374433):​n.202+5618C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,794 control chromosomes in the GnomAD database, including 17,437 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 0.44 (17437 hom., cov: 32)
• Consequence: LOC105374433 XR_925266.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 4 publications found

Genes affected

LOC105374433 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.439 AC: 66603 AN: 151674 Hom.: 17440 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.439 AC: 66596 AN: 151794 Hom.: 17437 Cov.: 32 AF XY: 0.433 AC XY: 32146 AN XY: 74212

African (AFR) AF: 0.170 AC: 6998 AN: 41248

American (AMR) AF: 0.465 AC: 7096 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1737 AN: 3468

East Asian (EAS) AF: 0.141 AC: 728 AN: 5162

South Asian (SAS) AF: 0.433 AC: 2082 AN: 4810

European-Finnish (FIN) AF: 0.540 AC: 5696 AN: 10554

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.594 AC: 40393 AN: 67970

Other (OTH) AF: 0.486 AC: 1025 AN: 2110

Alfa AF: 0.553 Hom.: 39170

Bravo AF: 0.421

Asia WGS AF: 0.262 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.085
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1442855; hg19: chr4-43323916;