chr14-78149250-T-C

Variant names:

• chr14-78149250-T-C
• rs4903712

Variant summary

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

The variant allele was found at a frequency of 0.196 in 152,078 control chromosomes in the GnomAD database, including 3,689 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 0.20 (3689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 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: 0.196 AC: 29776 AN: 151960 Hom.: 3687 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.196 AC: 29786 AN: 152078 Hom.: 3689 Cov.: 32 AF XY: 0.195 AC XY: 14493 AN XY: 74342

African (AFR) AF: 0.0694 AC: 2880 AN: 41498

American (AMR) AF: 0.193 AC: 2955 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1084 AN: 3472

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5172

South Asian (SAS) AF: 0.198 AC: 953 AN: 4818

European-Finnish (FIN) AF: 0.269 AC: 2841 AN: 10558

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18286 AN: 67962

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.254 Hom.: 8596

Bravo AF: 0.183

Asia WGS AF: 0.121 AC: 418 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.65
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4903712; hg19: chr14-78615593;