chr14-48968728-T-G

Variant names:

• chr14-48968728-T-G
• rs2352908
• XR_007064152.1:n.345+101064A>C

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+101064A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 151,964 control chromosomes in the GnomAD database, including 46,914 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 0.78 (46914 hom., cov: 30)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 3 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 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: 0.781 AC: 118542 AN: 151846 Hom.: 46907 Cov.: 30

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.780 AC: 118587 AN: 151964 Hom.: 46914 Cov.: 30 AF XY: 0.777 AC XY: 57742 AN XY: 74282

African (AFR) AF: 0.696 AC: 28821 AN: 41424

American (AMR) AF: 0.758 AC: 11579 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2570 AN: 5142

South Asian (SAS) AF: 0.669 AC: 3220 AN: 4812

European-Finnish (FIN) AF: 0.835 AC: 8827 AN: 10572

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57793 AN: 67960

Other (OTH) AF: 0.794 AC: 1675 AN: 2110

Alfa AF: 0.821 Hom.: 10714

Bravo AF: 0.771

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2352908; hg19: chr14-49437931;