chr14-78068563-G-T

Variant names:

• chr14-78068563-G-T
• rs3850370

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 0.688 in 152,020 control chromosomes in the GnomAD database, including 36,622 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 0.69 (36622 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104472 AN: 151902 Hom.: 36598 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.688 AC: 104532 AN: 152020 Hom.: 36622 Cov.: 31 AF XY: 0.684 AC XY: 50815 AN XY: 74316

African (AFR) AF: 0.539 AC: 22340 AN: 41424

American (AMR) AF: 0.721 AC: 11014 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2844 AN: 3472

East Asian (EAS) AF: 0.733 AC: 3798 AN: 5184

South Asian (SAS) AF: 0.647 AC: 3109 AN: 4802

European-Finnish (FIN) AF: 0.696 AC: 7353 AN: 10572

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51625 AN: 67970

Other (OTH) AF: 0.759 AC: 1602 AN: 2112

Alfa AF: 0.736 Hom.: 95570

Bravo AF: 0.686

Asia WGS AF: 0.681 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs3850370; hg19: chr14-78534906;