chr14-49140552-C-A

Variant names:

• chr14-49140552-C-A
• rs8008169
• XR_007064152.1:n.221+11278G>T

Variant summary

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

The XR_943837.3(LOC105378178):​n.221+11278G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,728 control chromosomes in the GnomAD database, including 11,038 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 (11038 hom., cov: 32)
• Consequence: LOC105378178 XR_943837.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.52 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: 0.367 AC: 55614 AN: 151612 Hom.: 11029 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.367 AC: 55645 AN: 151728 Hom.: 11038 Cov.: 32 AF XY: 0.367 AC XY: 27220 AN XY: 74168

African (AFR) AF: 0.276 AC: 11421 AN: 41430

American (AMR) AF: 0.530 AC: 8057 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3460

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5178

South Asian (SAS) AF: 0.243 AC: 1172 AN: 4814

European-Finnish (FIN) AF: 0.458 AC: 4821 AN: 10516

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27513 AN: 67806

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.368 Hom.: 1635

Bravo AF: 0.372

Asia WGS AF: 0.156 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.36
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs8008169; hg19: chr14-49607270;