14-46599121-T-G

Variant names:

• chr14-46599121-T-G
• rs1472242
• XR_001750753.1:n.814-1632A>C

Variant summary

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

The XR_943828.2(LOC105370481):​n.814-1632A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,666 control chromosomes in the GnomAD database, including 28,929 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 0.62 (28929 hom., cov: 32)
• Consequence: LOC105370481 XR_943828.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 1 publications found

Genes affected

LOC105370481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.615 AC: 93256 AN: 151548 Hom.: 28903 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.615 AC: 93330 AN: 151666 Hom.: 28929 Cov.: 32 AF XY: 0.619 AC XY: 45870 AN XY: 74128

African (AFR) AF: 0.620 AC: 25652 AN: 41406

American (AMR) AF: 0.588 AC: 8944 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3785 AN: 5140

South Asian (SAS) AF: 0.562 AC: 2712 AN: 4828

European-Finnish (FIN) AF: 0.721 AC: 7625 AN: 10582

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 40962 AN: 67734

Other (OTH) AF: 0.597 AC: 1257 AN: 2106

Alfa AF: 0.598 Hom.: 15512

Bravo AF: 0.608

Asia WGS AF: 0.587 AC: 2036 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1472242; hg19: chr14-47068324;