chr14-77261503-C-T

Variant names:

• chr14-77261503-C-T
• rs368855
• XR_007064276.1:n.1324+361C>T

Variant summary

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

The XR_007064276.1(LOC124903351):​n.1324+361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,128 control chromosomes in the GnomAD database, including 4,786 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 0.24 (4786 hom., cov: 33)
• Consequence: LOC124903351 XR_007064276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 5 publications found

Genes affected

LOC124903351 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35867 AN: 152010 Hom.: 4777 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.236 AC: 35902 AN: 152128 Hom.: 4786 Cov.: 33 AF XY: 0.241 AC XY: 17914 AN XY: 74364

African (AFR) AF: 0.197 AC: 8167 AN: 41478

American (AMR) AF: 0.313 AC: 4793 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1039 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3050 AN: 5162

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4818

European-Finnish (FIN) AF: 0.188 AC: 1995 AN: 10590

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14529 AN: 67994

Other (OTH) AF: 0.254 AC: 536 AN: 2114

Alfa AF: 0.227 Hom.: 3311

Bravo AF: 0.248

Asia WGS AF: 0.391 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.37
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs368855; hg19: chr14-77727846;