14-48909045-C-T

Variant names:

• chr14-48909045-C-T
• rs1986410
• XR_007064152.1:n.345+160747G>A

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+160747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,950 control chromosomes in the GnomAD database, including 6,720 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 0.29 (6720 hom., cov: 32)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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: 0.291 AC: 44153 AN: 151832 Hom.: 6714 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.291 AC: 44174 AN: 151950 Hom.: 6720 Cov.: 32 AF XY: 0.291 AC XY: 21627 AN XY: 74256

African (AFR) AF: 0.360 AC: 14932 AN: 41438

American (AMR) AF: 0.228 AC: 3471 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1183 AN: 3464

East Asian (EAS) AF: 0.169 AC: 871 AN: 5162

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4814

European-Finnish (FIN) AF: 0.282 AC: 2979 AN: 10570

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18243 AN: 67940

Other (OTH) AF: 0.302 AC: 640 AN: 2116

Alfa AF: 0.273 Hom.: 17744

Bravo AF: 0.287

Asia WGS AF: 0.237 AC: 822 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.18
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs1986410; hg19: chr14-49378248;