rs716308

Variant names:

• chr14-97776606-G-C
• rs716308
• XR_944186.4:n.503+2524G>C

Your query was ambiguous. Multiple possible variants found:

• chr14-97776606-G-C
• chr14-97776606-G-T

Variant summary

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

The XR_944186.4(LOC105370651):​n.503+2524G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,854 control chromosomes in the GnomAD database, including 28,773 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 0.61 (28773 hom., cov: 31)
• Consequence: LOC105370651 XR_944186.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 1 publications found

Genes affected

LOC105370651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.610 AC: 92506 AN: 151738 Hom.: 28752 Cov.: 31

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.610 AC: 92574 AN: 151854 Hom.: 28773 Cov.: 31 AF XY: 0.614 AC XY: 45576 AN XY: 74196

African (AFR) AF: 0.538 AC: 22255 AN: 41396

American (AMR) AF: 0.715 AC: 10921 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2340 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4742 AN: 5130

South Asian (SAS) AF: 0.676 AC: 3258 AN: 4818

European-Finnish (FIN) AF: 0.591 AC: 6225 AN: 10532

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40713 AN: 67918

Other (OTH) AF: 0.641 AC: 1351 AN: 2106

Alfa AF: 0.494 Hom.: 1468

Bravo AF: 0.617

Asia WGS AF: 0.759 AC: 2635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs716308; hg19: chr14-98242943;