chr14-48903598-A-C

Variant names:

• chr14-48903598-A-C
• rs2352904
• XR_007064152.1:n.345+166194T>G

Variant summary

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

The XR_007064152.1(LOC105378178):​n.345+166194T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,358 control chromosomes in the GnomAD database, including 23,771 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 0.56 (23771 hom., cov: 30)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 13 publications found

Genes affected

LOC105378178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.593 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: 0.557 AC: 84275 AN: 151242 Hom.: 23738 Cov.: 30

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.557 AC: 84358 AN: 151358 Hom.: 23771 Cov.: 30 AF XY: 0.555 AC XY: 41045 AN XY: 73902

African (AFR) AF: 0.494 AC: 20359 AN: 41216

American (AMR) AF: 0.601 AC: 9153 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1873 AN: 3462

East Asian (EAS) AF: 0.435 AC: 2242 AN: 5150

South Asian (SAS) AF: 0.399 AC: 1911 AN: 4792

European-Finnish (FIN) AF: 0.620 AC: 6442 AN: 10398

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40535 AN: 67814

Other (OTH) AF: 0.545 AC: 1145 AN: 2100

Alfa AF: 0.572 Hom.: 70564

Bravo AF: 0.555

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2352904; hg19: chr14-49372801;