14-94895874-C-G

Variant names:

• chr14-94895874-C-G
• rs10484048

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 0.163 in 152,184 control chromosomes in the GnomAD database, including 2,877 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 0.16 (2877 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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: 0.163 AC: 24759 AN: 152068 Hom.: 2885 Cov.: 33

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.163 AC: 24749 AN: 152184 Hom.: 2877 Cov.: 33 AF XY: 0.167 AC XY: 12413 AN XY: 74406

African (AFR) AF: 0.0560 AC: 2326 AN: 41554

American (AMR) AF: 0.222 AC: 3392 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2892 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4818

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10596

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

European-Non Finnish (NFE) AF: 0.176 AC: 11935 AN: 67980

Other (OTH) AF: 0.170 AC: 359 AN: 2114

Alfa AF: 0.0612 Hom.: 78

Bravo AF: 0.165

Asia WGS AF: 0.380 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.39
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10484048; hg19: chr14-95362211;