14-55951401-G-T

Variant names:

• chr14-55951401-G-T
• rs10151037
• XR_007064180.1:n.3852G>T

Variant summary

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

The XR_007064180.1(LOC102723670):​n.3852G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,208 control chromosomes in the GnomAD database, including 4,067 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 0.21 (4067 hom., cov: 33)
• Consequence: LOC102723670 XR_007064180.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 3 publications found

Genes affected

LOC102723670 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612704.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000259868	ENST00000612704.1	TSL:5	n.217-5754G>T		intron	N/A
	ENSG00000259868	ENST00000664335.2		n.323-6561G>T		intron	N/A
	ENSG00000259868	ENST00000729158.1		n.758-5754G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32121 AN: 152090 Hom.: 4060 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.211 AC: 32152 AN: 152208 Hom.: 4067 Cov.: 33 AF XY: 0.220 AC XY: 16380 AN XY: 74402

African (AFR) AF: 0.306 AC: 12716 AN: 41526

American (AMR) AF: 0.246 AC: 3766 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2287 AN: 5176

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4824

European-Finnish (FIN) AF: 0.236 AC: 2498 AN: 10578

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8553 AN: 68012

Other (OTH) AF: 0.196 AC: 414 AN: 2114

Alfa AF: 0.149 Hom.: 1207

Bravo AF: 0.217

Asia WGS AF: 0.346 AC: 1204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.37
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs10151037; hg19: chr14-56418119;