rs764602

Variant names:

• chr14-49011216-C-T
• rs764602
• XR_007064152.1:n.345+58576G>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+58576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,834 control chromosomes in the GnomAD database, including 12,832 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 (12832 hom., cov: 32)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• 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=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.365 AC: 55427 AN: 151716 Hom.: 12826 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.365 AC: 55428 AN: 151834 Hom.: 12832 Cov.: 32 AF XY: 0.371 AC XY: 27507 AN XY: 74196

African (AFR) AF: 0.103 AC: 4270 AN: 41488

American (AMR) AF: 0.429 AC: 6527 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3464

East Asian (EAS) AF: 0.0641 AC: 331 AN: 5166

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4820

European-Finnish (FIN) AF: 0.603 AC: 6367 AN: 10554

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33485 AN: 67808

Other (OTH) AF: 0.369 AC: 778 AN: 2110

Alfa AF: 0.451 Hom.: 8606

Bravo AF: 0.341

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs764602; hg19: chr14-49480419;