14-84869871-T-G

Variant names:

• chr14-84869871-T-G
• rs856675

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 0.225 in 152,046 control chromosomes in the GnomAD database, including 6,499 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 0.23 (6499 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• 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 (AFR) allele frequency at 95% confidence interval = 0.513 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: 0.225 AC: 34160 AN: 151928 Hom.: 6469 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.225 AC: 34234 AN: 152046 Hom.: 6499 Cov.: 32 AF XY: 0.217 AC XY: 16157 AN XY: 74352

African (AFR) AF: 0.519 AC: 21481 AN: 41422

American (AMR) AF: 0.129 AC: 1965 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3468

East Asian (EAS) AF: 0.0669 AC: 346 AN: 5172

South Asian (SAS) AF: 0.148 AC: 714 AN: 4830

European-Finnish (FIN) AF: 0.0616 AC: 652 AN: 10588

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8139 AN: 67972

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.188 Hom.: 4801

Bravo AF: 0.242

Asia WGS AF: 0.120 AC: 416 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.51
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs856675; hg19: chr14-85336215;